Contacts of the helix formed by residues 101 - 121 (chain C) in PDB entry 1PRC
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 101 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C THR* 2.6 41.8 + - - +
89C TYR 4.3 5.2 - - - +
90C CYS 3.6 15.9 - - - +
91C HIS 2.7 30.0 + - - +
92C ASP* 4.3 7.6 - - + +
93C GLU 5.2 0.8 - - - +
98C SER 4.8 1.4 + - - +
99C GLU 3.3 4.5 - - - +
100C ALA* 1.3 82.2 - - + +
102C TYR* 1.3 68.7 + - - +
103C PRO* 3.3 8.5 - - + -
104C TYR* 2.9 18.9 + - - +
105C VAL* 4.2 1.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 102 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C TYR* 3.8 5.2 + - - -
99C GLU 5.3 0.2 - - - -
100C ALA 3.8 3.6 + - - -
101C LYS* 1.3 71.1 - - - +
103C PRO* 1.3 87.5 - - + +
104C TYR 2.6 13.7 + - - -
105C VAL* 2.9 22.6 + - + +
106C VAL* 3.3 18.0 + - + +
288C SER* 3.6 25.1 - - - +
289C LEU* 4.0 3.1 - - + -
290C PRO* 3.6 36.8 - - + +
293C ARG* 4.0 6.8 + - - -
610C HEC 2.6 43.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 103 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C TYR* 3.5 59.2 - - + +
90C CYS* 4.0 8.8 - - - -
101C LYS* 3.5 5.4 - - + -
102C TYR* 1.3 122.5 - - + +
104C TYR* 1.3 60.6 + - - +
106C VAL* 4.1 2.9 - - + -
107C ALA* 3.0 25.8 + - - +
610C HEC 3.7 11.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 104 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C ASN* 3.1 34.8 + - - +
90C CYS* 3.4 23.8 - - + +
91C HIS* 3.7 25.8 - + - -
96C LEU 4.2 7.6 + - - -
97C ALA 4.3 4.4 + - - -
98C SER 3.8 19.3 - - - +
99C GLU* 3.8 22.9 - - + -
101C LYS 2.9 9.0 + - - +
102C TYR 2.6 7.3 + - - -
103C PRO* 1.3 76.8 - - - +
105C VAL* 1.3 68.7 + - + +
107C ALA* 3.3 4.3 - - - +
108C ARG* 2.9 44.1 + - - +
609C HEC 3.2 46.4 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 105 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C GLU* 4.0 36.6 - - - +
101C LYS 4.8 0.9 - - - +
102C TYR* 2.9 17.6 + - - +
104C TYR* 1.3 79.1 - - + +
106C VAL* 1.3 67.3 + - + +
108C ARG* 3.0 11.9 + - - +
109C ARG* 3.0 21.4 + - - +
285C LEU* 6.0 1.6 - - + -
288C SER* 4.0 28.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 106 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C TYR* 3.7 22.2 - - + +
103C PRO 4.0 2.9 - - - +
104C TYR 3.2 0.4 - - - -
105C VAL* 1.3 85.2 - - + +
107C ALA* 1.3 51.0 + - - +
108C ARG 2.8 3.6 - - - -
109C ARG* 2.7 27.8 + - - +
110C MET* 2.7 24.7 + - + +
285C LEU* 4.2 19.1 - - + -
288C SER* 4.5 9.0 - - - -
289C LEU* 3.9 24.9 - - + -
610C HEC 3.2 45.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 107 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C ILE* 5.6 0.6 - - + +
103C PRO 3.0 19.5 + - - +
104C TYR 3.3 5.2 - - - +
106C VAL* 1.3 78.2 - - - +
108C ARG* 1.3 58.4 + - - +
110C MET* 3.5 10.9 - - - +
111C LEU* 3.0 30.7 + - - +
609C HEC 3.6 40.8 - - + -
610C HEC 4.0 13.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 108 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C ASN* 3.6 22.6 + - - +
60C LYS* 3.7 22.6 - - - +
61C VAL* 3.8 22.2 - - + -
99C GLU* 3.0 31.9 + - - -
104C TYR* 2.9 21.8 + - - +
105C VAL* 3.2 13.6 - - - +
106C VAL 2.8 1.8 - - - -
107C ALA* 1.3 77.6 - - - +
109C ARG* 1.3 63.6 + - - +
111C LEU* 3.1 14.1 + - + +
112C GLU* 3.3 18.8 + - - +
609C HEC 2.4 60.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 109 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C VAL 3.0 9.6 + - - +
106C VAL 2.7 10.6 + - - +
108C ARG* 1.3 70.2 - - - +
110C MET* 1.3 55.4 + - + +
112C GLU* 2.7 53.6 + - - +
113C MET* 2.7 17.5 + - - +
280C ASN 2.9 24.7 + - - -
281C TYR* 3.5 42.4 + - + +
284C PRO* 5.8 2.4 - - - +
285C LEU* 4.1 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 110 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C VAL* 2.7 22.3 + - + +
107C ALA 3.5 4.5 - - - +
109C ARG* 1.3 78.4 - - + +
111C LEU* 1.3 56.7 + - - +
113C MET* 3.5 16.3 - - + +
114C THR* 2.8 36.8 + - - -
281C TYR 5.6 0.9 - - - +
282C LEU* 3.3 30.3 - - + -
285C LEU* 3.9 15.7 - - + -
610C HEC 2.3 95.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 111 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C VAL* 4.3 17.7 - - + -
62C LEU* 3.6 35.9 - - + -
73C THR* 5.1 1.3 - - + -
74C MET* 5.2 1.1 - - + -
77C ILE* 4.0 22.2 - - + -
107C ALA 3.0 20.4 + - - +
108C ARG* 3.1 9.2 + - - +
109C ARG 3.1 0.2 - - - -
110C MET* 1.3 76.9 - - - +
112C GLU* 1.3 63.5 + - - +
114C THR* 3.8 1.0 - - - -
115C ARG* 3.1 30.7 + - - +
328C LEU* 3.8 19.3 - - + -
609C HEC 4.7 18.2 - - + +
610C HEC 3.4 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 112 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C VAL* 4.0 20.8 - - + +
108C ARG* 3.3 16.8 + - - +
109C ARG* 2.7 52.6 + - - +
111C LEU* 1.3 72.8 - - - +
113C MET* 1.3 53.5 + - - +
115C ARG* 3.4 10.1 + - - +
116C ALA* 3.0 25.6 + - - +
281C TYR* 4.3 3.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 113 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C ARG 2.7 14.8 + - - +
110C MET* 3.5 22.2 - - + +
112C GLU* 1.3 70.4 - - - +
114C THR* 1.3 66.9 + - - +
116C ALA* 3.0 4.6 + - - +
117C ILE* 2.9 32.0 + - + +
277C LEU* 4.4 9.2 - - + -
281C TYR* 3.4 48.1 - - + -
282C LEU* 3.8 16.2 - - + -
610C HEC 3.3 61.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 114 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C MET 2.8 21.9 + - - -
111C LEU 3.8 3.6 - - - -
113C MET* 1.3 79.2 - - - +
115C ARG* 1.3 64.1 + - - +
116C ALA 3.0 1.2 + - - -
117C ILE* 3.1 9.1 + - - +
118C ASN* 3.1 37.1 + - - +
130C VAL* 3.7 17.0 - - + +
131C THR* 4.7 1.8 - - - -
328C LEU* 4.1 21.5 - - + +
610C HEC 3.3 40.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 115 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C VAL* 3.8 43.9 + - - +
62C LEU* 4.3 7.2 - - - +
64C ASN* 6.0 4.6 - - - +
111C LEU* 3.1 19.0 + - - +
112C GLU* 3.4 8.7 - - - +
114C THR* 1.3 81.7 - - - +
116C ALA* 1.3 54.8 + - - +
118C ASN* 4.0 1.6 - - - +
119C THR* 2.7 32.9 + - - -
327C GLU* 3.0 30.7 + - - +
328C LEU* 3.4 21.5 - - + -
331C ILE* 3.4 35.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 116 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C GLU 3.0 13.3 + - - +
113C MET* 3.0 10.5 + - - +
115C ARG* 1.3 76.2 - - - +
117C ILE* 1.3 68.5 + - + +
118C ASN 3.1 1.3 - - - -
119C THR* 4.3 1.1 - - - +
120C ASN* 2.8 40.0 + - - +
121C TRP* 3.6 10.6 + - + +
276C ASP* 6.1 0.4 - - - +
277C LEU* 5.9 0.4 - - + -
281C TYR* 3.5 25.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 117 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C MET* 2.9 29.2 + - + +
114C THR* 3.6 6.3 - - - +
116C ALA* 1.3 78.0 - - - +
118C ASN* 1.3 63.1 + - - +
121C TRP* 3.4 32.3 + - + +
125C VAL* 3.8 27.4 - - + +
130C VAL* 3.7 26.9 - - + -
273C MET* 4.3 9.2 - - - -
277C LEU* 3.6 43.3 - - + -
610C HEC 4.4 6.7 - - + -
612C HEC 4.2 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 118 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C THR* 3.1 17.3 + - - +
115C ARG 4.3 0.4 - - - +
116C ALA 3.1 0.6 - - - -
117C ILE* 1.3 79.3 - - - +
119C THR* 1.3 58.7 + - - +
122C THR* 3.8 12.7 - - - +
125C VAL* 4.0 7.1 - - - +
126C ALA 5.6 0.7 - - - +
129C GLY* 2.8 33.2 - - - -
130C VAL* 2.8 32.0 + - - +
322C LEU* 3.6 11.7 - - + +
328C LEU* 3.1 29.6 + - - +
329C GLY* 3.7 13.2 - - - -
330C PRO* 3.7 14.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 119 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C ARG 2.7 22.4 + - - -
116C ALA* 3.1 4.0 + - - -
118C ASN* 1.3 79.2 - - - +
120C ASN* 1.3 72.2 + - - +
122C THR* 3.8 14.2 + - - +
330C PRO* 3.3 9.4 - - + +
331C ILE* 3.1 52.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 120 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C ALA* 2.8 30.4 + - + +
119C THR* 1.3 83.4 - - - +
121C TRP* 1.3 71.8 + - + +
122C THR* 3.3 12.3 + - - -
123C GLN* 4.7 5.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 121 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C ALA* 3.8 16.5 - - + +
117C ILE* 3.4 28.4 + - + +
120C ASN* 1.3 85.2 - - + +
122C THR* 1.3 59.5 + - - +
123C GLN* 3.0 4.5 - - + +
124C HIS* 3.0 7.0 + - + -
125C VAL* 2.8 25.1 + - - +
269C TRP* 4.1 26.0 - + + -
272C ARG* 3.8 18.4 - - + -
273C MET* 3.7 55.6 - - + +
276C ASP* 2.9 44.5 + - + +
277C LEU* 4.7 3.4 - - + +
281C TYR* 6.1 0.2 - - - -
322M PRO* 5.0 8.3 - - + -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il