Contacts of the helix formed by residues 97 - 114 (chain C) in PDB entry 2X1L
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 ASP 97 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C ARG* 2.9 22.6 + - - +
92C PHE 4.6 2.4 - - - +
93C ILE* 3.9 1.9 - - - +
94C ARG* 2.9 43.3 + - - +
96C SER* 1.3 83.3 + - - +
98C ALA* 1.3 66.0 + - - +
99C ASP* 3.3 17.0 - - - +
100C HIS* 3.2 15.3 + - + +
101C TYR* 3.3 12.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 98 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C SER 3.6 2.9 + - - -
97C ASP* 1.3 72.8 - - - +
99C ASP* 1.3 61.2 + - - +
101C TYR* 3.2 19.6 + - - +
102C GLU* 3.3 17.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 99 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C ARG* 2.9 43.4 + - - -
97C ASP* 3.4 8.7 - - - +
98C ALA* 1.3 75.5 - - - +
100C HIS* 1.3 64.0 + - - +
102C GLU* 3.5 14.0 + - - +
103C ALA* 3.0 28.2 + - - +
239C THR* 3.7 11.3 - - + +
243C PHE 4.3 5.4 - - - +
244C PRO* 4.9 0.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 100 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C ILE* 4.5 2.7 - - + +
94C ARG 4.3 7.9 - - - +
95C THR* 3.3 33.3 - - + +
97C ASP* 3.2 12.5 + - + +
99C ASP* 1.3 82.0 + - - +
101C TYR* 1.3 56.1 + - - +
104C SER* 2.7 48.5 + - - -
217C VAL* 4.8 2.7 - - + -
232C ASP* 2.6 43.8 + - - -
235C THR* 3.8 2.0 - - - -
236C ASN* 3.3 33.4 - - + +
239C THR* 3.0 30.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 101 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C HIS* 3.2 22.5 + + - -
95C THR 3.6 19.3 - - - -
96C SER* 3.9 13.7 - - - -
97C ASP 3.3 15.8 + - - -
98C ALA* 3.2 13.1 + - - +
100C HIS* 1.3 77.1 - - - +
102C GLU* 1.3 65.2 + - + +
104C SER* 3.4 5.9 + - - -
105C LYS* 3.0 47.2 + - - +
215C TRP* 5.2 5.2 - - - -
216C GLY 3.9 7.4 + - - -
217C VAL* 3.9 23.7 - - + +
218C PRO* 3.7 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 102 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C ALA* 3.3 12.0 + - - +
99C ASP* 3.6 15.4 - - - +
101C TYR* 1.3 79.5 - - + +
103C ALA* 1.3 56.3 + - - +
105C LYS* 3.3 11.1 + - + +
106C ALA* 3.0 30.1 + - - +
244C PRO* 4.3 21.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 103 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C ASP 3.0 16.3 + - - +
100C HIS 3.8 1.6 - - - +
102C GLU* 1.3 76.2 - - - +
104C SER* 1.3 62.0 + - - +
106C ALA 3.3 0.5 + - - -
107C ILE* 3.1 22.3 + - - +
235C THR* 3.7 5.8 - - + +
239C THR* 3.3 26.5 - - - +
243C PHE* 3.5 42.1 - - + +
244C PRO* 4.1 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 104 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C HIS* 2.7 45.6 + - - -
101C TYR 3.7 3.8 - - - -
103C ALA* 1.3 75.1 - - - +
105C LYS* 1.3 62.5 + - - +
107C ILE* 3.3 6.6 - - - +
108C TRP* 3.2 17.7 + - - +
217C VAL* 4.0 10.1 - - - -
227C MET* 3.3 30.5 - - - +
232C ASP* 3.7 12.8 - - - +
235C THR* 4.0 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 105 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C TYR* 3.0 49.0 + - - +
102C GLU* 3.3 9.5 + - + +
104C SER* 1.3 75.1 - - - +
106C ALA* 1.3 57.7 + - - +
108C TRP* 3.6 2.6 + - - +
109C LYS* 3.1 27.4 + - - +
217C VAL* 4.4 1.8 - - + -
218C PRO* 4.3 22.1 - - - +
220C PRO* 4.0 26.7 - - + +
227C MET* 3.9 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 106 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C GLU 3.0 17.3 + - - +
103C ALA 3.7 3.8 - - - +
104C SER 3.3 0.2 - - - -
105C LYS* 1.3 76.2 - - - +
107C ILE* 1.3 60.2 + - - +
109C LYS* 3.4 9.7 + - - +
110C ARG* 3.0 33.0 + - + +
243C PHE* 4.0 6.5 - - + -
244C PRO* 3.5 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 107 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C ALA 3.1 15.5 + - - +
104C SER* 3.3 13.0 - - - +
106C ALA* 1.3 74.1 - - - +
108C TRP* 1.3 67.9 + - - +
110C ARG* 3.4 4.6 + - - +
111C MET* 3.1 36.0 + - + +
231C VAL* 5.2 6.1 - - + +
235C THR* 3.4 24.9 - - + +
238C LEU* 3.7 26.2 - - + -
243C PHE* 4.0 10.7 - - + -
274C TRP* 4.3 13.2 - - + -
277C PHE* 4.8 9.6 - - + +
278C LEU* 4.4 9.2 - - + -
281C ALA* 4.0 19.1 - - + -
283C LEU* 4.6 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 108 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C SER 3.2 17.7 + - - +
105C LYS* 3.6 5.2 - - - +
107C ILE* 1.3 78.6 - - + +
109C LYS* 1.3 58.1 + - - +
111C MET* 3.4 10.7 + - + -
112C ALA* 3.0 32.7 + - + +
117C ILE* 3.5 34.4 - - + +
164C TYR* 4.1 9.6 - + + -
208C ILE* 3.3 50.5 - - + -
209C SER* 4.3 3.1 - - - -
219C VAL* 3.5 35.1 - - + +
220C PRO* 4.0 18.8 - - + -
222C HIS* 6.1 0.2 - - - -
227C MET* 3.7 35.4 - - + -
231C VAL* 4.4 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 109 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C LYS 3.1 18.9 + - - +
106C ALA* 3.5 9.9 - - - +
107C ILE 3.3 0.2 - - - -
108C TRP* 1.3 79.5 - - - +
110C ARG* 1.3 56.4 + - + +
112C ALA* 3.9 4.7 - - - +
113C ASP* 2.9 67.7 + - - +
220C PRO* 5.7 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 110 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C ALA* 3.0 21.9 + - - +
107C ILE* 3.7 6.3 - - - +
108C TRP 3.3 0.2 - - - -
109C LYS* 1.3 77.8 - - + +
111C MET* 1.3 56.9 + - - +
113C ASP* 3.6 5.7 + - - +
114C ALA* 3.1 27.0 + - - +
243C PHE* 4.1 21.5 - - - -
244C PRO 5.2 1.8 + - - -
246C THR* 3.7 28.5 + - - +
280C SER 4.1 3.2 - - - +
281C ALA* 3.1 40.0 + - + +
282C GLY 4.2 5.3 + - - -
283C LEU* 3.5 20.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 111 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C ILE* 3.1 33.2 + - + +
108C TRP* 4.1 10.1 - - + -
110C ARG* 1.3 75.1 - - - +
112C ALA* 1.3 62.5 + - - +
114C ALA* 3.4 2.1 + - - +
115C GLY 3.4 3.5 + - - -
116C ASP* 3.0 27.7 + - - +
117C ILE* 3.8 19.5 - - + -
166C PHE* 3.7 13.9 - - + -
208C ILE* 5.5 2.9 - - + -
231C VAL* 4.4 22.0 - - + -
277C PHE* 3.6 50.0 - - + +
280C SER* 3.4 21.1 - - - +
281C ALA* 4.3 4.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 112 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C TRP* 3.0 25.8 + - + +
109C LYS* 3.9 5.4 - - - +
111C MET* 1.3 75.2 - - - +
113C ASP* 1.3 62.1 + - - +
115C GLY* 3.1 18.2 + - - -
117C ILE* 3.6 28.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 113 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C LYS* 2.9 54.3 + - - +
110C ARG* 3.9 5.2 - - - +
112C ALA* 1.3 78.3 - - - +
114C ALA* 1.3 59.6 + - - +
115C GLY* 3.2 2.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 114 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C ARG 3.1 18.5 + - - +
111C MET 3.6 7.4 - - - +
112C ALA 3.2 0.4 - - - -
113C ASP* 1.3 75.8 - - - +
115C GLY* 1.3 57.9 + - - +
116C ASP* 3.5 11.3 - - - +
280C SER* 3.5 20.6 - - - +
602C CXS 3.4 19.6 - - - +
----------------------------------------------------------
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