Contacts of the helix formed by residues 103 - 117 (chain A) in PDB entry 1GQC
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 ARG 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A ARG* 5.2 1.6 - - - +
101A MET 4.1 7.9 - - - +
102A ILE* 1.3 80.0 - - - +
104A PRO* 1.3 62.4 - - + +
105A ARG* 3.0 6.1 - - + +
106A ASP* 2.6 72.5 + - - +
107A VAL* 3.4 5.4 + - - +
217A VAL* 3.8 1.0 - - - +
218A ALA* 2.6 46.3 + - - +
219A ALA 2.8 23.2 + - - -
220A THR* 3.4 16.9 - - + +
221A GLY 5.0 1.4 - - - +
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Residues in contact with PRO 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ARG* 3.4 34.1 - - + +
39A GLN* 3.8 38.1 - - + +
40A VAL* 4.0 10.7 - - + +
102A ILE* 3.5 10.3 - - + +
103A ARG* 1.3 82.0 - - + +
105A ARG* 1.3 76.8 + - - +
107A VAL* 3.1 8.0 + - + +
108A GLU* 3.0 26.3 + - - +
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Residues in contact with ARG 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A GLN* 4.0 19.0 + - - +
41A ALA* 5.2 1.4 - - - +
103A ARG* 2.8 8.6 + - + -
104A PRO* 1.3 89.7 - - - +
106A ASP* 1.3 65.0 + - - +
108A GLU* 2.6 50.7 + - - +
109A THR* 3.1 24.2 + - - -
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Residues in contact with ASP 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ILE* 4.8 5.8 - - + +
103A ARG* 2.6 64.0 + - - +
105A ARG* 1.3 72.9 - - - +
107A VAL* 1.3 64.2 + - - +
109A THR* 3.2 11.2 + - - -
110A LEU* 3.1 20.8 + - - +
125A LEU* 3.9 23.9 - - + +
217A VAL* 3.6 25.3 - - + +
218A ALA 5.1 0.2 + - - -
220A THR* 4.2 5.5 - - - +
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Residues in contact with VAL 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ILE* 4.6 4.5 - - + -
40A VAL* 3.8 25.8 - - + -
93A ILE* 4.0 35.6 - - + +
95A LEU* 4.0 14.6 - - + -
102A ILE* 3.9 31.6 - - + -
103A ARG 4.0 4.3 - - - +
104A PRO* 3.1 8.8 + - + +
106A ASP* 1.3 76.7 - - - +
108A GLU* 1.3 59.0 + - - +
110A LEU* 3.3 12.1 - - + +
111A LEU* 3.0 24.6 + - - +
125A LEU* 5.2 0.7 - - - -
175A ILE* 4.5 3.6 - - + -
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Residues in contact with GLU 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A GLN 3.7 3.6 - - - +
40A VAL* 3.9 14.6 - - + -
41A ALA* 2.9 35.6 + - - +
104A PRO 3.0 14.6 + - - +
105A ARG* 2.6 53.1 + - - +
106A ASP 3.2 0.2 - - - -
107A VAL* 1.3 74.0 - - - +
109A THR* 1.3 61.6 + - - +
111A LEU* 3.2 6.9 + - - +
112A GLN* 2.8 31.2 + - - +
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Residues in contact with THR 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A ARG 3.1 14.8 + - - -
106A ASP* 3.3 13.5 + - - -
108A GLU* 1.3 77.6 - - - +
110A LEU* 1.3 61.9 + - - +
112A GLN* 3.2 7.8 + - + +
113A GLY* 3.0 21.1 + - - -
125A LEU* 5.1 0.2 - - + -
215A PHE* 4.4 28.2 - - + -
216A GLU 5.5 2.2 - - - +
217A VAL* 5.0 11.7 - - + +
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Residues in contact with LEU 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A ILE* 4.6 8.5 - - + -
106A ASP 3.1 9.0 + - - +
107A VAL* 3.3 13.7 - - + +
109A THR* 1.3 80.5 - - - +
111A LEU* 1.3 60.8 + - - +
113A GLY* 3.3 9.9 + - - -
114A MET* 3.3 16.7 + - - +
123A ALA* 3.8 9.4 - - + +
124A THR* 3.4 46.0 - - - +
125A LEU* 3.7 12.7 - - + +
175A ILE* 3.4 33.4 - - + -
176A TYR 4.1 5.8 - - - -
177A ALA* 3.9 23.1 - - + -
215A PHE* 4.7 5.6 - - + -
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Residues in contact with LEU 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A ALA* 4.0 8.3 - - + -
40A VAL* 4.7 3.4 - - + -
41A ALA 3.8 20.0 - - - +
42A GLY 4.1 3.1 - - - +
43A VAL* 3.9 22.4 - - + -
91A ILE* 4.0 21.8 - - + -
93A ILE* 3.9 17.9 - - + +
107A VAL 3.0 12.0 + - - +
108A GLU* 3.7 8.5 - - - +
110A LEU* 1.3 73.7 - - - +
112A GLN* 1.3 64.4 + - - +
114A MET* 3.2 5.7 + - - +
115A ARG* 3.0 61.5 + - - +
177A ALA* 5.6 0.7 - - - -
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Residues in contact with GLN 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A GLU 2.8 16.9 + - - +
109A THR* 3.4 9.6 - - + +
111A LEU* 1.3 73.9 - - - +
113A GLY* 1.3 60.6 + - - +
115A ARG* 4.4 12.5 - - - +
116A ASP* 2.7 67.4 + - - +
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Residues in contact with GLY 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A THR 3.0 10.9 + - - -
110A LEU 3.3 2.2 + - - -
111A LEU 3.2 0.4 - - - -
112A GLN* 1.3 77.9 - - - +
114A MET* 1.3 63.0 + - - +
116A ASP* 3.4 5.8 + - - +
117A ASP* 3.3 21.8 + - - +
120A LEU* 4.3 6.9 - - - +
213A ARG* 5.6 0.2 + - - -
215A PHE* 3.6 34.7 - - - -
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Residues in contact with MET 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A ILE* 3.6 23.6 - - + -
110A LEU 3.3 14.1 + - - +
111A LEU* 3.2 9.3 + - - +
113A GLY* 1.3 75.3 - - - +
115A ARG* 1.3 62.4 + - - +
117A ASP 2.9 25.8 - - - +
120A LEU* 3.4 29.8 - - - +
121A PRO 3.7 14.8 - - - +
123A ALA* 3.6 28.3 - - + -
177A ALA* 3.8 18.2 - - + +
178A TYR 3.9 6.3 - - - -
179A ARG* 3.3 38.2 + - - +
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Residues in contact with ARG 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A SER* 2.8 50.7 + - - +
3A ALA* 3.6 12.7 - - - +
41A ALA 5.0 0.2 + - - -
42A GLY* 3.0 36.0 + - - -
91A ILE* 4.4 6.1 - - + -
111A LEU* 3.0 42.4 + - - +
112A GLN* 4.0 14.6 - - - +
114A MET* 1.3 79.3 - - - +
116A ASP* 1.3 61.0 + - - +
117A ASP 3.3 0.7 + - - -
118A PRO* 4.0 9.9 - - - +
179A ARG* 4.6 4.5 - - - +
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Residues in contact with ASP 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A GLN* 2.7 54.2 + - - +
113A GLY* 3.9 6.7 - - - +
114A MET 3.3 0.4 - - - -
115A ARG* 1.3 72.0 - - - +
117A ASP* 1.3 60.7 + - + +
118A PRO* 3.9 4.7 - - - +
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Residues in contact with ASP 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A GLY 3.3 9.5 + - - +
114A MET 2.9 12.8 + - - +
115A ARG 3.1 0.4 - - - -
116A ASP* 1.3 82.6 - - + +
118A PRO* 1.3 60.5 - - - +
119A ALA* 2.8 26.1 + - - +
120A LEU* 3.0 23.0 + - + +
179A ARG* 3.1 2.8 + - - -
213A ARG* 2.8 35.6 + - - +
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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
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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