Contacts of the helix formed by residues 100 - 112 (chain C) in PDB entry 1I2M
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 ASN 100 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C ASP* 4.7 3.1 + - - +
70C GLU* 5.7 0.4 - - - +
71C LYS* 4.0 16.2 - - - +
97C THR 4.6 2.2 + - - -
98C TYR 3.3 1.0 - - - -
99C LYS* 1.3 78.7 - - + +
101C VAL* 1.3 65.5 + - - +
102C PRO* 3.3 3.4 - - - -
103C ASN* 2.8 42.9 + - - +
104C TRP* 2.9 56.6 + - + +
303D GLN* 2.8 32.2 + - - +
354D ALA* 5.3 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 101 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C ILE* 4.0 19.6 - - + +
90C PHE* 4.7 4.0 - - + -
97C THR 4.5 0.9 - - - +
98C TYR* 3.1 51.6 + - + +
100C ASN* 1.3 75.8 - - - +
102C PRO* 1.3 73.7 - - + +
104C TRP* 3.3 15.1 + - + +
105C HIS* 2.9 23.0 + - + +
119C LEU* 4.2 17.5 - - + -
141C LYS* 4.3 13.2 - - - +
144C LEU* 4.4 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 102 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C TYR* 5.1 6.1 - - + +
99C LYS 3.4 14.8 - - - +
100C ASN 3.5 0.4 - - - -
101C VAL* 1.3 97.0 - - + +
103C ASN* 1.3 57.5 + - - +
105C HIS* 3.4 7.1 + - + +
106C ARG* 2.9 35.2 + - - +
141C LYS* 6.0 1.1 - - - +
371D MET* 4.5 6.1 - - + -
373D THR* 4.5 10.7 - - + +
374D ASN* 3.4 32.5 - - - +
409D GLN* 3.4 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 103 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C LYS* 5.0 2.6 + - - +
100C ASN* 2.8 41.0 + - - +
102C PRO* 1.3 75.5 - - - +
104C TRP* 1.3 66.0 + - - +
106C ARG* 3.3 5.2 + - - +
107C ASP* 3.0 34.2 + - - +
303D GLN* 3.7 11.6 + - - +
323D TYR* 5.2 3.4 - - + -
354D ALA* 4.1 13.5 - - - +
355D SER* 3.1 19.1 + - - -
371D MET* 3.1 29.8 - - - +
374D ASN* 6.0 0.4 - - - +
408D GLY 5.6 1.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 104 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C VAL* 3.8 16.9 - - + +
17C GLY* 3.4 25.8 - - - -
18C ASP* 3.3 38.4 - - - -
70C GLU* 2.9 30.2 + - + +
71C LYS* 3.8 10.5 - - - -
80C TYR* 3.4 21.3 + - - -
88C ILE* 3.7 24.7 - - + -
89C MET 4.5 2.0 - - - -
97C THR 4.1 11.7 - - - -
100C ASN* 2.9 44.8 + - + +
101C VAL* 3.6 18.6 - - + +
103C ASN* 1.3 75.2 - - - +
105C HIS* 1.3 62.5 + - - +
107C ASP* 3.3 7.2 + - - +
108C LEU* 3.0 32.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 105 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C ILE* 4.1 6.4 - - + +
101C VAL* 2.9 17.9 + - + +
102C PRO* 3.5 8.4 - - + +
104C TRP* 1.3 78.2 - - - +
106C ARG* 1.3 63.5 + - + +
108C LEU* 3.4 2.9 + - - +
109C VAL* 3.1 36.6 + - + +
117C ILE* 3.9 9.9 - - + +
141C LYS* 5.4 1.8 + - - -
143C ASN* 4.0 23.9 + - + -
144C LEU* 3.4 49.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 106 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C PRO 2.9 21.0 + - - +
103C ASN* 3.7 4.7 - - - +
105C HIS* 1.3 77.8 - - + +
107C ASP* 1.3 59.4 + - - +
109C VAL* 3.4 6.7 + - - +
110C ARG* 2.9 30.1 + - - +
323D TYR* 3.3 36.9 + - + +
371D MET* 3.6 15.2 - - - +
373D THR* 2.6 45.7 + - + +
382D ASP 5.2 1.4 + - - -
384D ASP* 2.8 40.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 107 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C GLU* 6.1 0.3 - - - +
80C TYR* 3.5 30.3 + - + -
103C ASN* 3.0 26.4 + - - +
104C TRP* 3.3 4.8 + - - +
106C ARG* 1.3 75.8 - - - +
108C LEU* 1.3 58.1 + - - +
110C ARG* 2.8 22.4 + - - +
111C VAL* 2.9 35.3 + - - +
320D ARG* 3.1 19.5 + - - -
323D TYR* 2.6 29.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 108 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C VAL* 3.9 19.3 - - + -
16C VAL* 4.8 7.6 - - + -
80C TYR* 3.9 36.3 - - + -
86C ALA* 3.9 20.6 - - + -
88C ILE* 4.1 24.0 - - + -
104C TRP 3.0 22.4 + - - +
105C HIS 3.8 1.6 - - - +
107C ASP* 1.3 77.0 - - - +
109C VAL* 1.3 57.5 + - - +
112C CYS* 2.9 33.5 + - - +
113C GLU 3.3 4.8 + - - +
115C ILE* 4.4 8.2 - - + +
117C ILE* 3.8 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 109 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C HIS* 3.1 39.2 + - + +
106C ARG* 4.0 6.1 - - - +
108C LEU* 1.3 76.8 - - - +
110C ARG* 1.3 51.8 + - - +
113C GLU* 2.7 63.1 + - - +
117C ILE* 4.4 7.6 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
77C ASP* 2.9 33.3 + - - -
80C TYR* 5.6 1.0 - - - -
106C ARG 2.9 17.3 + - - +
107C ASP* 2.8 30.4 + - - +
109C VAL* 1.3 73.8 - - - +
111C VAL* 1.3 68.4 + - - +
113C GLU* 2.5 22.4 - - - +
320D ARG* 3.2 15.2 - - - +
322D GLU* 3.9 21.6 + - - +
323D TYR* 2.9 33.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 111 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C ASP* 3.4 26.2 - - + +
80C TYR* 3.9 18.6 - - + -
81C ILE* 3.6 39.0 - - + +
107C ASP 2.9 20.0 + - - +
110C ARG* 1.3 108.0 - - - +
112C CYS* 1.3 59.5 + - - +
113C GLU* 4.3 3.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 112 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C TYR* 3.2 40.6 - - - -
81C ILE* 4.7 3.4 - - - -
83C ALA* 3.9 15.0 - - - +
108C LEU* 2.9 17.8 + - - +
111C VAL* 1.3 76.2 - - - +
113C GLU* 1.3 74.1 + - - +
114C ASN 3.5 1.7 + - - -
115C ILE* 3.5 40.5 - - + +
----------------------------------------------------------
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