Contacts of the helix formed by residues 88 - 109 (chain A) in PDB entry 1GTA
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 GLU 88 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A GLY* 3.1 29.2 - - - +
84A GLY* 3.9 5.9 - - - -
85A CYS* 2.9 20.9 + - - +
87A LYS* 1.3 74.1 - - - +
89A ARG* 1.3 65.9 + - - +
91A GLU* 3.3 8.4 - - + +
92A ILE* 3.1 32.3 + - + +
144A ASN* 3.8 19.4 + - - +
149A THR* 5.9 0.2 - - - +
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Residues in contact with ARG 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ARG* 4.9 9.9 + - - +
82A LEU* 3.4 24.6 - - + +
83A GLY* 3.5 6.3 - - - +
84A GLY* 3.6 35.7 + - - +
85A CYS* 3.0 11.1 + - - +
86A PRO* 3.4 34.6 - - + +
88A GLU* 1.3 79.0 - - - +
90A ALA* 1.3 55.7 + - - +
92A ILE* 3.5 3.3 + - - +
93A SER* 3.1 27.9 + - - -
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Residues in contact with ALA 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A PRO 2.8 18.6 + - - +
87A LYS* 3.8 7.0 - - + +
88A GLU 3.4 0.2 - - - -
89A ARG* 1.3 73.5 - - - +
91A GLU* 1.3 54.4 + - - +
93A SER* 3.2 7.5 + - - +
94A MET* 2.8 35.3 + - - +
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Residues in contact with GLU 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LYS* 3.2 16.2 + - - +
88A GLU* 3.3 14.8 - - + +
90A ALA* 1.3 74.1 - - - +
92A ILE* 1.3 65.6 + - - +
94A MET* 3.4 20.2 + - - +
95A LEU* 3.1 30.5 + - - +
136A ARG* 2.9 35.7 + - - +
144A ASN* 3.4 23.1 - - - +
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Residues in contact with ILE 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ARG* 4.4 4.9 - - - +
81A MET 3.9 15.0 - - - +
82A LEU 3.7 25.4 - - - +
83A GLY* 3.9 4.9 - - - +
88A GLU* 3.1 23.1 + - + +
89A ARG 3.8 3.8 - - - +
91A GLU* 1.3 80.9 - - - +
93A SER* 1.4 59.2 + - - +
95A LEU* 3.5 9.8 + - + +
96A GLU* 3.3 20.4 + - - +
144A ASN* 3.8 29.2 - - - +
149A THR* 4.2 15.9 - - + +
150A HIS* 3.8 28.0 - - + +
151A PRO* 3.9 8.9 - - + +
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Residues in contact with SER 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ARG* 3.0 27.2 + - - -
89A ARG 3.1 14.3 + - - -
90A ALA* 3.2 10.5 + - - -
92A ILE* 1.4 71.1 - - - +
94A MET* 1.3 65.1 + - - +
96A GLU* 3.2 15.4 + - - +
97A GLY* 3.1 19.9 + - - -
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Residues in contact with MET 94 (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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90A ALA 2.8 20.4 + - - +
91A GLU* 3.4 24.0 + - - +
93A SER* 1.3 73.1 - - - +
95A LEU* 1.3 60.2 + - + +
97A GLY* 3.4 1.5 + - - +
98A ALA* 2.9 31.1 + - + +
136A ARG* 5.9 0.9 - - - -
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Residues in contact with LEU 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A GLU* 3.1 22.1 + - - +
92A ILE* 3.8 11.0 - - + +
93A SER 3.3 0.2 - - - -
94A MET* 1.3 75.4 - - + +
96A GLU* 1.3 62.4 + - - +
98A ALA* 3.5 5.4 + - + +
99A VAL* 2.8 35.1 + - - +
133A PHE* 4.3 8.7 - - + -
136A ARG* 3.8 43.5 - - + +
143A LEU* 4.0 34.1 - - + +
144A ASN* 4.0 15.3 - - + +
149A THR* 5.1 0.9 - - - +
151A PRO* 4.0 15.9 - - + -
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Residues in contact with GLU 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A MET* 4.3 13.6 - - - +
73A ARG* 2.8 43.2 + - - +
92A ILE 3.3 7.7 + - - +
93A SER* 3.2 17.3 + - - +
95A LEU* 1.3 80.7 - - - +
97A GLY* 1.3 56.2 + - - +
99A VAL* 3.3 0.7 + - - -
100A LEU* 3.1 26.5 + - + +
150A HIS* 2.6 34.8 + - - +
151A PRO* 4.4 3.5 - - + +
154A MET* 3.4 34.5 - - + +
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Residues in contact with GLY 97 (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 SER 3.1 9.7 + - - -
94A MET* 3.9 2.5 - - - -
96A GLU* 1.3 76.5 - - - +
98A ALA* 1.3 63.2 + - - +
100A LEU* 3.7 13.1 - - - +
101A ASP* 3.1 27.5 + - - +
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Residues in contact with ALA 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A MET* 2.9 23.6 + - + +
95A LEU* 4.0 3.4 - - + +
97A GLY* 1.3 71.9 - - - +
99A VAL* 1.4 59.1 + - - +
101A ASP* 3.5 22.8 - - - +
102A ILE* 4.0 4.2 + - - +
129A MET* 5.9 0.7 - - - +
132A MET* 4.8 16.0 - - + +
133A PHE* 3.6 28.5 - - + -
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Residues in contact with VAL 99 (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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95A LEU 2.8 27.5 + - - +
96A GLU* 4.1 1.6 - - - +
98A ALA* 1.4 72.7 - - - +
100A LEU* 1.3 67.1 + - + +
102A ILE* 3.2 7.9 + - + +
103A ARG* 3.0 23.2 + - + +
133A PHE* 3.6 25.6 - - + -
143A LEU* 5.1 1.1 - - + -
151A PRO* 4.3 16.8 - - + +
154A MET* 3.6 45.1 - - + +
155A LEU* 4.2 14.6 - - + +
158A ALA* 4.6 6.2 - - + +
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Residues in contact with LEU 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A MET* 4.1 30.5 - - + -
96A GLU* 3.1 23.8 + - + +
97A GLY* 3.2 10.7 + - - +
99A VAL* 1.3 75.8 - - + +
101A ASP* 1.3 56.9 + - - +
103A ARG* 4.4 9.0 - - + +
104A TYR* 2.8 77.2 + - + +
154A MET* 3.7 19.3 - - + -
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Residues in contact with ASP 101 (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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97A GLY 3.1 15.7 + - - +
98A ALA* 3.5 16.5 - - - +
100A LEU* 1.3 74.0 - - - +
102A ILE* 1.3 60.6 + - + +
104A TYR* 5.6 0.2 - - - -
105A GLY* 3.2 19.2 + - - -
122A PHE* 4.8 0.7 - - - -
129A MET* 3.9 28.2 - - + +
132A MET* 6.0 1.9 - - - +
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Residues in contact with ILE 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ALA 4.4 5.6 - - - +
99A VAL* 3.2 8.3 + - - +
101A ASP* 1.3 74.6 - - - +
103A ARG* 1.3 62.8 + - - +
105A GLY* 3.3 8.7 + - - -
106A VAL* 3.3 11.8 + - - +
122A PHE* 3.9 9.1 - - + -
126A LEU* 4.0 11.0 - - + -
129A MET* 3.8 29.8 - - + -
130A LEU* 3.9 23.8 - - + -
133A PHE* 3.7 30.5 - - + -
155A LEU* 4.7 9.9 - - + -
158A ALA* 4.2 13.7 - - + -
159A LEU* 6.0 0.4 - - + -
162A VAL* 3.8 28.7 - - + -
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Residues in contact with ARG 103 (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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11A LYS* 5.4 0.8 - - - +
12A GLY* 4.0 17.8 + - - +
99A VAL* 3.0 18.6 + - + +
100A LEU* 4.1 9.9 - - + +
102A ILE* 1.3 77.0 - - - +
104A TYR* 1.4 72.2 + - + +
106A VAL* 3.4 12.9 + - - +
107A SER* 3.3 16.7 + - - -
154A MET 6.0 0.2 - - - +
157A ASP* 3.4 26.7 + - - +
158A ALA* 4.2 20.4 - - + +
161A VAL* 3.7 28.0 - - - +
203A LEU* 3.4 20.4 + - - +
204A GLN* 3.0 30.9 + - - +
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Residues in contact with TYR 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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13A LEU* 3.8 26.1 - - + +
68A SER* 4.2 13.9 + - - -
69A MET* 4.3 14.5 - - + +
100A LEU* 2.8 53.5 + - + +
103A ARG* 1.4 82.1 - - + +
105A GLY* 1.4 55.8 + - - +
106A VAL 3.4 0.2 - - - -
107A SER* 3.6 10.8 - - - -
108A ARG* 2.9 35.1 + - + +
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Residues in contact with GLY 105 (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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101A ASP 3.2 22.0 + - - -
102A ILE 3.6 2.0 - - - -
103A ARG 3.1 1.4 - - - -
104A TYR* 1.4 74.2 - - - +
106A VAL* 1.4 63.8 + - - +
108A ARG* 3.7 14.6 + - - +
109A ILE* 3.6 23.4 + - - +
122A PHE* 4.0 18.1 - - - -
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Residues in contact with VAL 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ILE 3.3 14.1 + - - +
103A ARG* 3.7 13.9 - - - +
104A TYR 3.4 0.2 - - - -
105A GLY* 1.4 72.7 - - - +
107A SER* 1.3 59.0 + - - +
109A ILE* 3.2 11.1 + - + +
110A ALA* 2.9 25.0 + - + +
115A PHE* 6.2 0.2 - - + -
122A PHE* 4.0 21.0 - - + -
161A VAL* 4.0 17.3 - - + -
162A VAL* 4.3 11.2 - - + -
165A MET* 4.7 7.2 - - - -
204A GLN* 3.3 22.4 - - - +
210A PHE* 3.7 30.3 - - + -
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Residues in contact with SER 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ARG* 3.3 15.2 + - - -
104A TYR* 3.6 16.6 - - - -
106A VAL* 1.3 75.5 - - - +
108A ARG* 1.3 65.9 + - - +
110A ALA* 3.1 18.0 + - - +
111A TYR* 4.0 10.6 - - - -
204A GLN* 2.8 31.6 + - - +
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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
----------------------------------------------------------
104A TYR* 2.9 24.2 + - + +
105A GLY* 3.9 12.3 - - - +
106A VAL 3.4 0.4 - - - -
107A SER* 1.3 73.1 - - - +
109A ILE* 1.3 73.5 + - + +
110A ALA 3.7 5.0 - - - +
112A SER* 5.3 2.8 - - - -
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Residues in contact with ILE 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 GLY 3.6 10.3 - - - +
106A VAL* 3.4 14.4 - - - +
107A SER 3.1 0.6 - - - -
108A ARG* 1.3 95.5 - - + +
110A ALA* 1.3 66.8 + - - +
112A SER* 3.7 15.0 + - - -
115A PHE* 3.8 27.2 - - + +
118A LEU* 3.7 45.1 - - + +
119A LYS* 3.9 7.4 - - - +
122A PHE* 3.7 37.0 - - + -
165A MET* 5.0 2.2 - - + -
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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
------------------------------------------------------------
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