Contacts of the helix formed by residues 103 - 123 (chain A) in PDB entry 1GV3
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 ILE 103 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ALA* 3.4 41.7 - - + +
78A LEU* 4.9 0.9 - - + -
80A LYS* 4.3 17.5 - - + +
81A HIS* 3.6 18.4 - - + -
84A LEU* 4.0 22.7 - - + -
99A VAL* 4.1 3.1 - - + -
100A PRO* 3.5 16.2 - - + +
102A ASP* 1.3 94.3 - - - +
104A ARG* 1.3 66.0 + - - +
105A THR 3.4 2.2 - - - -
106A THR* 3.3 11.2 + - - +
107A VAL* 3.0 35.4 + - + +
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Residues in contact with ARG 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A LEU* 2.9 41.6 + - + +
97A ASN* 3.3 26.9 + - - +
99A VAL* 3.0 27.7 + - + +
100A PRO* 3.1 11.2 + - - +
101A GLU* 3.5 42.6 + - - +
103A ILE* 1.3 77.8 - - - +
105A THR* 1.3 65.6 + - - +
107A VAL* 3.3 2.8 + - - +
108A ARG* 3.0 22.2 + - + +
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Residues in contact with THR 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A GLU 5.0 0.8 + - - -
103A ILE 3.4 0.4 - - - -
104A ARG* 1.3 78.3 - - - +
106A THR* 1.3 59.3 + - - +
108A ARG* 3.2 12.6 + - - +
109A ASN* 2.9 51.1 + - - +
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Residues in contact with THR 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ASN* 4.3 9.9 - - + +
74A LEU* 5.1 0.6 - - - +
77A ALA* 3.8 24.5 - - + -
102A ASP 4.8 1.7 + - - -
103A ILE* 3.3 18.2 + - - +
104A ARG 3.3 0.4 - - - -
105A THR* 1.3 79.7 - - - +
107A VAL* 1.3 57.0 + - - +
109A ASN* 4.9 2.0 - - - +
110A ASN* 2.9 53.4 + - - +
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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
----------------------------------------------------------
74A LEU* 4.3 21.8 - - + -
77A ALA* 4.7 4.9 - - + -
78A LEU* 4.4 10.1 - - + -
84A LEU* 5.5 0.2 - - + -
92A LEU* 4.2 32.1 - - + -
93A LEU* 3.7 8.7 - - + +
96A LEU* 4.6 6.7 - - + -
99A VAL* 4.2 13.0 - - + -
103A ILE* 3.0 37.6 + - + +
104A ARG 3.8 4.0 - - - +
106A THR* 1.3 73.2 - - - +
108A ARG* 1.3 60.6 + - - +
111A GLY* 2.7 33.1 + - - -
112A GLY 3.7 0.2 + - - -
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Residues in contact with ARG 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A LEU* 4.0 12.3 - - - +
96A LEU* 3.9 24.7 - - + +
104A ARG* 3.0 14.8 + - - +
105A THR* 3.4 15.9 - - - +
107A VAL* 1.3 77.3 - - - +
109A ASN* 1.3 66.7 + - - +
112A GLY* 3.0 25.6 + - - -
183A PRO* 5.6 0.4 - - - +
185A GLN 4.2 4.2 - - - +
186A ASP* 2.7 42.7 + - - +
190A MET* 3.8 21.1 - - - +
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Residues in contact with ASN 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A TYR* 4.4 0.5 - - - -
105A THR* 2.9 37.4 + - - +
106A THR* 4.1 2.6 - - - +
108A ARG* 1.3 91.3 + - - +
110A ASN* 1.3 63.8 + - - +
113A GLY* 2.9 20.8 + - - -
184A ASN* 5.5 1.2 - - - +
185A GLN* 3.3 16.7 + - - +
186A ASP* 4.7 4.3 - - - +
162B PHE* 3.5 57.0 - - + +
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Residues in contact with ASN 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A TYR* 3.4 41.1 - - - +
73A ASN* 3.2 35.1 + - - +
74A LEU* 4.0 12.3 - - + +
106A THR* 2.9 43.5 + - - +
109A ASN* 1.3 81.1 - - - +
111A GLY* 1.3 61.8 + - - +
113A GLY 4.2 0.2 - - - +
114A HIS* 2.9 30.0 + - - +
162B PHE* 5.0 4.1 - - - -
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Residues in contact with GLY 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LEU* 4.1 17.5 - - - +
89A VAL* 3.5 17.6 - - - +
93A LEU* 3.9 8.5 - - - -
107A VAL* 2.7 23.1 + - - -
110A ASN* 1.3 73.9 - - - +
112A GLY* 1.3 57.6 + - - +
114A HIS* 3.3 1.4 + - - +
115A LEU* 2.9 31.4 + - - +
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Residues in contact with GLY 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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93A LEU* 3.9 15.0 - - - +
107A VAL 3.7 0.4 + - - -
108A ARG 3.0 16.8 + - - -
111A GLY* 1.3 75.9 - - - +
113A GLY* 1.3 56.1 + - - +
115A LEU* 3.3 1.3 + - - -
116A ASN* 2.8 37.5 + - - +
185A GLN 3.2 23.3 - - - -
187A ASN* 5.0 2.7 - - - -
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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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67A HIS* 4.3 0.2 - - - -
70A TYR* 3.8 16.7 - - - -
109A ASN 2.9 18.1 + - - -
110A ASN 3.3 2.0 + - - -
111A GLY 3.3 0.2 - - - -
112A GLY* 1.3 77.2 - - - +
114A HIS* 1.3 59.5 + - - +
117A HIS* 2.8 32.1 + - - +
185A GLN* 3.5 24.1 - - - +
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Residues in contact with HIS 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 3.6 28.7 - - + +
34A GLY 4.9 0.8 + - - -
38A ALA* 4.4 12.9 - - + +
39A GLU 3.3 33.2 + - - -
41A PRO* 3.8 4.9 - - + -
67A HIS* 2.8 32.9 + - - -
70A TYR* 4.0 4.1 - - + +
71A VAL* 3.6 19.4 - - + +
74A LEU* 4.4 4.5 - - + -
89A VAL* 4.1 12.1 - - + -
110A ASN 2.9 18.1 + - - +
111A GLY* 3.6 6.7 - - - +
113A GLY* 1.3 74.1 - - - +
115A LEU* 1.3 64.2 + - - +
118A THR* 2.9 46.1 + - - -
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Residues in contact with LEU 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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26A ILE* 4.1 11.0 - - + -
27A GLY* 3.5 36.6 - - - +
33A LEU* 3.9 15.2 - - + +
89A VAL* 4.2 7.9 - - + -
90A GLU* 4.4 8.5 - - + +
93A LEU* 3.9 9.9 - - + -
111A GLY 2.9 16.7 + - - +
112A GLY 3.8 2.9 - - - +
114A HIS* 1.3 77.1 - - - +
116A ASN* 1.3 62.9 + - - +
118A THR* 3.2 4.0 + - - -
119A ILE* 3.1 29.9 + - + +
187A ASN* 3.4 31.6 - - - +
189A ILE* 3.7 24.5 - - + -
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Residues in contact with ASN 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 GLY 2.8 22.4 + - - +
113A GLY 4.1 0.7 - - - +
115A LEU* 1.3 71.7 - - - +
117A HIS* 1.3 56.8 + - - +
119A ILE* 3.3 6.8 + - - +
120A PHE* 3.0 25.3 + - - +
166A TRP* 3.6 30.5 - - + +
168A TRP* 3.5 19.6 - - + -
185A GLN* 3.0 45.5 + - - +
186A ASP 3.6 6.1 + - - -
187A ASN* 2.7 32.2 - - - +
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Residues in contact with HIS 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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62A HIS* 3.0 26.0 + + - -
67A HIS* 3.4 29.6 - + + +
70A TYR* 3.6 14.5 - + - -
113A GLY 2.8 26.9 + - - +
116A ASN* 1.3 76.2 - - - +
118A THR* 1.3 66.0 + - - +
120A PHE* 3.4 6.1 - + - +
121A TRP* 3.0 41.0 + + - +
166A TRP* 3.7 14.3 - + - -
185A GLN* 3.6 24.2 + - - -
200A ASP* 3.3 2.1 + - - -
1238A MN 2.2 33.1 + - - -
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Residues in contact with THR 118 (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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27A GLY* 4.1 12.3 - - - +
28A PHE* 3.8 33.9 - - + -
33A LEU* 4.1 4.6 - - + +
41A PRO* 3.6 8.8 - - + +
67A HIS* 3.4 9.6 - - - -
114A HIS* 2.9 43.6 + - - -
115A LEU* 3.2 8.0 + - - -
117A HIS* 1.3 78.2 - - - +
119A ILE* 1.3 64.3 + - - +
121A TRP* 3.7 8.4 + - - +
122A GLN* 3.2 27.6 + - - +
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Residues in contact with ILE 119 (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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26A ILE* 4.0 29.4 - - + +
27A GLY* 4.2 6.3 - - - -
115A LEU* 3.1 23.3 + - + +
116A ASN 3.5 5.4 - - - +
118A THR* 1.3 76.8 - - - +
120A PHE* 1.3 62.8 + - - +
122A GLN* 3.2 22.1 + - - +
123A ILE* 3.3 23.8 + - + +
168A TRP* 4.5 15.7 - - + -
187A ASN* 4.5 4.5 - - - +
195A PRO* 4.2 19.5 - - + +
196A ILE 4.6 3.6 - - - +
197A MET* 5.1 1.3 - - - -
233A ARG* 3.7 34.8 - - - +
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Residues in contact with PHE 120 (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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54A ILE* 4.9 3.8 - - + -
62A HIS* 3.8 24.2 - + - -
116A ASN 3.0 13.6 + - - +
117A HIS* 3.2 11.4 + + - +
119A ILE* 1.3 76.9 - - - +
121A TRP* 1.3 87.4 + + - +
123A ILE* 3.3 23.8 + - + +
124A MET* 3.6 30.2 - - + +
166A TRP* 3.7 19.7 - + + -
198A GLY 3.6 20.0 - - - -
199A ASN* 3.6 15.5 - - - -
200A ASP* 4.1 9.2 - - + -
217A TYR* 3.6 21.8 - - - -
221A TRP* 3.6 16.2 - + - -
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Residues in contact with TRP 121 (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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41A PRO* 5.1 7.6 - - + -
42A PRO 5.6 1.8 - - - +
43A LEU* 3.8 10.1 - - + -
44A PRO* 4.1 21.1 - - + +
45A TYR* 2.8 30.7 + - - -
59A MET* 3.5 32.5 - - + -
62A HIS* 3.5 38.4 - + + -
63A HIS* 3.6 41.0 - + + -
67A HIS* 2.9 30.1 + + - -
117A HIS* 3.0 31.1 + + + -
118A THR* 4.2 7.6 - - - +
119A ILE 3.4 0.4 - - - -
120A PHE* 1.3 96.7 - + - +
122A GLN* 1.3 59.9 + - + +
124A MET* 3.6 7.7 + - + +
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Residues in contact with GLN 122 (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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27A GLY 2.8 28.3 + - - +
28A PHE* 3.5 33.9 - - + -
29A ILE 5.5 0.7 + - - -
44A PRO* 4.7 13.2 - - + -
118A THR* 3.2 22.0 + - - +
119A ILE* 3.2 8.3 + - - +
121A TRP* 1.3 73.3 - - + +
123A ILE* 1.3 58.7 + - + +
124A MET 3.2 10.4 + - - +
226A ASN* 3.5 18.9 + - - -
229A GLU* 3.5 32.5 - - + +
233A ARG* 5.0 4.1 - - - +
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Residues in contact with ILE 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ILE* 3.3 16.4 + - + +
120A PHE* 3.3 18.4 - - + +
122A GLN* 1.3 76.9 - - + +
124A MET* 1.3 60.9 + - + +
196A ILE 4.1 5.4 - - - +
197A MET* 3.9 8.1 - - + -
198A GLY 3.4 40.6 - - - +
221A TRP* 3.9 15.2 - - + -
225A VAL* 3.7 9.5 - - - +
226A ASN* 2.9 25.7 + - - -
229A GLU* 4.5 4.0 - - + -
230A ILE* 4.0 17.7 - - + -
233A ARG* 3.8 29.4 - - - +
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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