Contacts of the helix formed by residues 97 - 114 (chain C) in PDB entry 1G3I
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).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B LYS* 5.8 4.0 + - - -
95C GLU* 3.4 19.1 + - - +
96C VAL* 1.3 84.1 - - - +
98C SER* 1.3 63.4 + - - +
99C ILE 3.1 0.2 - - - -
100C ILE* 3.2 9.1 + - - +
101C ARG* 3.1 40.0 + - - +
284C PRO* 5.8 1.4 - - - +
285C LEU* 3.9 14.0 - - - +
290C THR 5.8 0.2 - - - -
291C VAL* 3.4 30.7 - - + +
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Residues in contact with SER 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C LYS* 4.2 12.4 + - - -
86C PHE* 4.0 9.4 - - - -
95C GLU* 2.6 31.1 + - - +
96C VAL 2.9 1.7 + - - -
97C ASP* 1.3 77.7 - - - +
99C ILE* 1.3 56.0 + - - +
101C ARG* 2.6 37.6 + - - +
102C ASP* 2.6 30.6 + - - -
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Residues in contact with ILE 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C ILE* 4.3 5.6 - - + +
81C VAL* 3.8 33.4 - - + -
85C LYS* 6.0 0.7 - - - +
86C PHE* 3.5 34.1 - - + -
96C VAL* 3.5 12.8 - - + +
98C SER* 1.3 84.8 + - - +
100C ILE* 1.3 69.5 + - + +
102C ASP* 3.4 7.2 + - - +
103C LEU* 3.0 20.4 + - - +
254C VAL* 3.9 34.3 - - + -
256C ILE* 5.4 2.2 - - + -
282C LEU* 4.0 22.4 - - + -
285C LEU* 4.1 7.9 - - + -
305C PHE* 6.4 0.2 - - + -
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Residues in contact with ILE 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C ASP 3.2 3.6 + - - +
99C ILE* 1.3 80.6 - - + +
101C ARG* 1.3 66.2 + - - +
103C LEU* 3.5 7.1 - - + +
104C THR* 2.9 27.5 + - - +
248C VAL* 5.0 7.4 - - + -
254C VAL* 4.7 6.3 - - + -
285C LEU* 3.8 23.6 - - + -
291C VAL* 3.2 19.5 - - + -
298C VAL* 3.1 33.2 - - + -
299C LYS 5.8 0.2 - - - -
300C THR* 3.3 35.2 - - + +
303C ILE* 4.7 9.0 - - + -
305C PHE* 4.6 10.3 - - + -
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Residues in contact with ARG 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C GLU* 4.1 23.0 + - - +
97C ASP* 3.1 34.9 + - - +
98C SER* 2.6 28.7 + - - +
100C ILE* 1.3 71.6 - - - +
102C ASP* 1.3 65.0 + - - +
104C THR* 2.9 16.1 + - - -
105C ASP* 3.0 14.7 + - - +
291C VAL* 4.5 1.2 - - - +
292C SER* 3.3 26.6 + - - +
293C THR* 3.7 24.0 - - + +
294C LYS* 5.1 3.6 - - + +
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Residues in contact with ASP 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C ILE* 4.5 21.2 - - + +
81C VAL* 5.9 1.9 - - - +
85C LYS* 4.4 15.2 + - - -
98C SER* 2.6 27.1 + - - +
99C ILE* 3.8 5.8 + - - +
101C ARG* 1.3 75.0 - - - +
103C LEU* 1.3 62.7 + - - +
105C ASP* 3.1 14.5 + - - +
106C SER* 2.8 23.4 + - - -
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Residues in contact with LEU 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C PRO* 3.5 37.5 - - + +
78C PHE 4.0 2.0 - - - +
79C ILE* 3.1 28.2 - - + +
99C ILE 3.0 18.4 + - - +
100C ILE* 3.5 10.5 - - + +
102C ASP* 1.3 75.1 - - - +
104C THR* 1.3 64.9 + - - +
106C SER* 2.8 17.3 + - - -
107C ALA* 2.8 10.6 + - - +
248C VAL* 3.7 25.4 - - + -
252C GLY* 4.3 7.4 - - - -
253C ILE 3.9 2.5 - - - +
254C VAL* 3.9 20.0 - - + -
303C ILE* 4.1 15.0 - - + -
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Residues in contact with THR 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C ILE 2.9 12.3 + - - -
101C ARG 2.9 7.5 + - - -
103C LEU* 1.3 77.6 - - - +
105C ASP* 1.3 63.7 + - - +
107C ALA* 2.9 19.7 + - + +
108C MET* 3.2 5.9 + - - +
244C ALA* 5.6 1.6 - - + -
245C ILE* 5.0 7.4 - - + +
248C VAL* 3.3 19.3 - - + +
293C THR* 3.3 31.5 - - - +
295C HIS* 3.9 24.6 - - + -
298C VAL* 3.4 22.3 - - + +
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Residues in contact with ASP 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C ARG* 3.0 15.1 + - - +
102C ASP* 3.1 18.5 - - - +
104C THR* 1.3 75.4 - - - +
106C SER* 1.3 65.6 + - - +
108C MET* 3.3 15.9 + - - +
109C LYS* 3.8 4.9 + - - +
293C THR* 6.1 0.2 - - - -
294C LYS* 3.2 36.4 + - - +
295C HIS* 3.3 16.2 + - - -
292D SER* 5.0 4.7 - - - -
297D MET* 4.3 28.9 - - + +
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Residues in contact with SER 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C PRO* 4.8 6.0 - - - +
78C PHE 4.0 23.1 + - - -
79C ILE* 5.8 0.7 - - - -
102C ASP 2.8 10.6 + - - -
103C LEU* 2.8 14.5 + - - -
105C ASP* 1.3 72.0 - - - +
107C ALA* 1.3 66.2 + - - +
108C MET 2.9 1.6 + - - -
109C LYS* 3.2 21.5 + - - +
110C LEU* 3.1 20.1 + - - +
297D MET* 5.8 1.8 - - - +
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Residues in contact with ALA 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C PRO* 4.0 19.9 - - + +
103C LEU 2.8 5.2 + - - +
104C THR* 2.9 14.4 - - - +
106C SER* 1.3 76.6 - - - +
108C MET* 1.3 63.3 + - - +
110C LEU* 3.4 3.8 - - - +
111C VAL* 3.0 22.3 + - - +
244C ALA* 3.8 18.8 - - + +
247C ALA* 4.9 1.3 - - + +
248C VAL* 3.1 31.4 - - + -
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Residues in contact with MET 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C THR 3.2 3.2 + - - +
105C ASP 3.6 8.1 - - - +
106C SER 2.9 1.8 + - - -
107C ALA* 1.3 74.0 - - - +
109C LYS* 1.3 71.1 + - - +
110C LEU 2.5 3.3 + - - -
111C VAL* 2.7 6.0 + - - -
112C ARG* 2.7 33.9 + - + -
240C LEU* 3.9 33.4 - - + -
241C LYS* 4.1 23.3 - - + +
244C ALA* 3.5 22.2 - - + -
295C HIS* 3.4 39.9 - - + +
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Residues in contact with LYS 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C ASP 3.8 5.4 + - - +
106C SER* 3.2 19.9 + - - +
108C MET* 1.3 76.8 - - - +
110C LEU* 1.3 57.4 + - - +
112C ARG* 3.8 10.5 - - - +
113C GLN* 2.9 39.1 + - + +
290D THR* 4.2 16.6 + - - +
297D MET* 5.5 14.6 - - + +
299D LYS* 3.8 30.2 - - + +
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Residues in contact with LEU 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C ASN* 3.7 48.2 - - - +
76C ALA 4.1 1.8 - - - -
77C PRO* 4.0 26.0 - - + -
106C SER* 3.1 12.2 + - - +
107C ALA* 3.4 10.5 - - - +
108C MET 2.5 4.6 + - - -
109C LYS* 1.3 76.6 - - - +
111C VAL* 1.3 69.9 + - + +
113C GLN* 3.3 19.8 + - - +
114C GLN* 3.3 22.3 + - - +
247C ALA* 5.7 3.8 - - + -
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Residues in contact with VAL 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C ALA 3.0 9.2 + - - +
108C MET* 2.7 7.8 + - - +
110C LEU* 1.3 77.3 - - + +
112C ARG* 1.3 70.5 + - + +
114C GLN* 2.9 33.0 + - - +
115C GLU* 3.2 16.8 + - + +
240C LEU* 4.2 31.6 - - + +
243C LYS* 3.3 35.2 - - + +
244C ALA* 3.9 8.1 - - + +
247C ALA* 4.7 8.1 - - + -
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Residues in contact with ARG 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C MET* 2.7 30.1 + - + +
109C LYS* 3.8 9.4 - - - +
111C VAL* 1.3 76.5 - - - +
113C GLN* 1.3 57.2 - - - +
115C GLU* 2.6 35.3 + - + +
116C ILE* 3.2 33.1 + - + +
240C LEU* 4.5 21.8 - - + +
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Residues in contact with GLN 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C ASN* 5.9 0.2 + - - -
109C LYS* 2.9 26.5 + - + +
110C LEU* 3.7 15.4 + - - +
112C ARG* 1.3 77.3 - - - +
114C GLN* 1.3 62.8 + - - +
115C GLU 3.3 0.7 + - - -
116C ILE* 3.2 31.9 - - + +
117C ALA* 4.0 4.7 + - - +
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Residues in contact with GLN 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C ASN* 3.3 33.2 + - - +
110C LEU* 3.3 20.6 + - - +
111C VAL* 2.9 33.1 - - - +
113C GLN* 1.3 83.2 - - + +
115C GLU* 1.3 63.1 + - - +
117C ALA* 4.0 16.3 - - - +
118C LYS* 4.6 6.1 + - - +
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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
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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) + - + + + + + -
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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