Contacts of the helix formed by residues 86 - 103 (chain A) in PDB entry 2GTL
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 86 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A ASN 5.0 0.2 - - - +
83A LEU* 2.6 19.3 + - + +
85A ASP* 1.3 86.3 + - - +
87A THR* 1.3 67.4 + - - +
88A LEU* 2.7 6.5 + - - +
89A VAL* 2.8 27.1 + - + +
90A LEU 3.6 1.3 + - - -
28D ALA 4.4 1.4 - - - -
29D HIS* 3.3 46.7 + - - +
32D VAL* 3.6 26.1 - - + +
128H THR* 5.3 1.4 + - - -
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Residues in contact with THR 87 (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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12A ARG* 4.2 2.0 - - - +
83A LEU 3.7 2.0 + - - -
84A LEU 4.5 2.6 + - - +
85A ASP 3.5 1.3 + - - -
86A ASP* 1.3 73.8 - - - +
88A LEU* 1.3 56.7 + - - -
90A LEU* 2.8 15.6 + - - +
91A GLN* 2.7 35.3 + - - +
131G TYR 3.2 22.7 + - - -
132G ASP* 3.3 20.1 + - - +
133G ALA* 3.2 16.7 + - - +
134G LEU* 3.2 46.7 - - + +
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Residues in contact with LEU 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ASP 2.7 5.3 + - - +
87A THR* 1.3 80.8 + - - +
89A VAL* 1.3 61.8 + - + +
91A GLN* 3.6 19.6 + - - +
92A SER* 3.4 17.8 + - - -
64D PRO* 4.1 24.4 - - + +
125G PRO* 4.1 27.4 - - + +
131G TYR* 4.4 28.7 - - + +
133G ALA* 4.6 9.4 - - + -
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Residues in contact with VAL 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LEU* 3.7 23.3 - - + -
86A ASP* 2.8 24.3 + - + +
88A LEU* 1.3 72.3 - - + +
90A LEU* 1.3 69.2 + - - +
92A SER* 2.9 15.3 + - - -
93A HIS* 2.9 13.0 + - - +
32D VAL* 5.3 12.1 - - + -
64D PRO* 4.2 23.6 - - + +
67D GLY* 4.1 10.1 - - - +
68D ALA* 3.5 28.7 - - - +
71D GLN* 5.1 2.0 - - + +
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Residues in contact with LEU 90 (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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80A LEU* 3.9 33.7 - - + +
83A LEU* 3.5 28.6 - - + +
84A LEU* 3.8 34.8 - - + -
86A ASP 3.6 1.6 + - - -
87A THR* 2.8 11.4 + - - +
89A VAL* 1.3 79.8 - - - +
91A GLN* 1.3 53.3 + - - +
94A LEU* 2.7 58.3 + - + +
141A ARG* 5.3 4.0 - - - +
142A LEU* 4.1 11.2 - - + -
134G LEU* 4.4 17.3 - - + -
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Residues in contact with GLN 91 (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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87A THR 2.7 18.2 + - - +
88A LEU* 3.6 19.3 - - - +
89A VAL 3.2 0.2 - - - -
90A LEU* 1.3 76.3 - - - +
92A SER* 1.3 61.0 + - - +
94A LEU* 3.8 8.8 - - - +
95A GLY* 3.5 11.3 + - - -
141A ARG* 4.4 21.8 + - - +
145A ARG* 4.6 13.8 + - - +
133G ALA* 4.2 19.2 - - - +
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Residues in contact with SER 92 (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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88A LEU 3.4 8.8 + - - -
89A VAL 2.9 9.0 + - - -
91A GLN* 1.3 76.3 - - - +
93A HIS* 1.3 58.5 + - - +
94A LEU 2.9 1.3 - - - -
95A GLY* 2.7 23.0 + - - -
96A HIS* 2.9 12.4 + - - +
64D PRO* 4.5 9.9 - - - -
65D GLU* 4.3 18.9 + - - +
68D ALA* 3.9 15.5 - - - +
72D ARG* 5.3 0.9 + - - -
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Residues in contact with HIS 93 (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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76A GLY* 4.5 5.9 + - - -
79A LEU* 3.5 30.1 - - + +
80A LEU* 3.6 23.3 - - + +
83A LEU* 4.2 9.6 - - + -
89A VAL 2.9 13.9 + - - +
90A LEU 4.2 1.1 - - - +
92A SER* 1.3 76.4 - - - +
94A LEU* 1.3 57.0 + - - +
96A HIS* 3.7 12.0 - + - -
97A LEU* 2.8 53.0 + - + +
100A GLN* 5.4 0.4 - - - -
68D ALA* 4.0 8.6 - - + +
72D ARG* 3.4 45.8 + - + +
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Residues in contact with LEU 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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80A LEU* 3.3 29.4 - - + -
90A LEU* 2.7 27.2 + - + +
91A GLN* 3.8 8.1 - - - +
92A SER 2.9 0.2 - - - -
93A HIS* 1.3 78.9 - - - +
95A GLY* 1.3 63.8 + - - +
97A LEU* 3.4 6.0 + - + +
98A ALA* 3.3 15.6 + - - +
141A ARG* 3.7 23.6 - - - +
142A LEU* 3.7 31.0 - - + +
145A ARG* 3.9 25.0 - - + +
146A ILE* 3.8 28.0 - - + +
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Residues in contact with GLY 95 (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 GLN 3.5 3.6 + - - -
92A SER 2.7 9.9 + - - -
94A LEU* 1.3 75.3 - - - +
96A HIS* 1.3 55.9 + - - -
97A LEU 3.0 1.6 - - - -
98A ALA* 2.6 32.1 + - - +
99A ASP* 3.0 12.4 + - - +
145A ARG* 3.3 32.3 - - - +
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Residues in contact with HIS 96 (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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92A SER* 2.9 10.5 + - - +
93A HIS* 3.5 11.7 - + - +
95A GLY* 1.3 73.8 - - - +
97A LEU* 1.3 62.4 + - - +
99A ASP* 3.5 12.4 + - - +
100A GLN* 3.1 47.1 + - + +
55D ARG* 3.5 31.8 + - - +
72D ARG* 3.3 42.6 + - - +
160D HEM 3.2 36.6 + - - -
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Residues in contact with LEU 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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76A GLY* 5.0 3.8 - - - +
80A LEU* 3.8 28.5 - - + -
93A HIS* 2.8 37.7 + - + +
94A LEU 3.5 7.0 - - - +
95A GLY 3.0 0.2 - - - -
96A HIS* 1.3 75.3 - - - +
98A ALA* 1.3 62.3 + - - +
100A GLN* 3.7 18.7 + - - +
101A HIS* 3.1 32.4 + - + -
146A ILE* 3.4 35.0 - - + +
160A HEM 4.1 33.0 - - + -
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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
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94A LEU 3.3 4.7 + - - +
95A GLY 2.6 18.2 + - - +
97A LEU* 1.3 70.7 - - - +
99A ASP* 1.3 60.3 + - - +
100A GLN 3.0 1.1 - - - -
101A HIS* 2.5 28.9 + - - +
102A ILE* 2.9 21.5 + - + +
145A ARG* 4.0 12.1 - - - +
146A ILE* 2.9 39.0 - - - +
149A ASP* 5.6 2.5 - - - +
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Residues in contact with ASP 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 GLY* 3.0 13.3 + - - +
96A HIS* 3.8 13.8 - - - +
98A ALA* 1.3 76.5 - - - +
100A GLN* 1.3 62.2 + - + +
101A HIS 3.1 0.9 + - - -
102A ILE* 4.0 19.1 - - - +
103A GLN* 3.3 39.7 + - - +
145A ARG* 5.9 0.3 + - - -
55D ARG* 5.8 1.6 + - - -
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Residues in contact with GLN 100 (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 HIS* 5.4 0.5 - - - -
96A HIS* 3.1 34.8 + - + +
97A LEU* 3.9 25.8 - - - +
98A ALA 2.9 1.0 + - - -
99A ASP* 1.3 77.2 - - + +
101A HIS* 1.3 66.6 + - + +
103A GLN* 4.5 1.8 - - - +
104A ARG* 2.8 39.7 + - - +
160A HEM 4.2 32.7 + - + +
100D GLN* 5.1 1.0 + - - -
160D HEM 3.0 32.7 + - - +
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Residues in contact with HIS 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 LEU* 3.1 25.5 + - + +
98A ALA* 2.5 17.8 + - - +
100A GLN* 1.3 79.4 - - + +
102A ILE* 1.3 61.0 + - - -
103A GLN 3.3 2.0 - - - -
104A ARG* 3.3 20.8 + - - +
107A VAL* 3.8 4.8 - - + +
112A PHE* 3.6 19.3 - + + -
146A ILE* 5.0 0.7 - - + -
150A LEU* 3.3 28.6 - - + +
160A HEM 1.9 97.7 + + + -
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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
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98A ALA* 2.9 22.2 + - + +
99A ASP* 3.3 25.1 + - - +
101A HIS* 1.3 76.6 - - - +
103A GLN* 1.3 61.5 + - + +
104A ARG 3.0 12.1 + - - +
105A LYS* 4.5 1.9 + - - -
146A ILE 5.2 0.7 - - - +
149A ASP* 4.0 40.6 - - + +
150A LEU* 4.1 20.0 - - + +
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Residues in contact with GLN 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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99A ASP* 3.3 25.7 + - - +
100A GLN* 5.4 1.0 - - - +
101A HIS 3.3 0.4 - - - +
102A ILE* 1.3 78.7 - - + +
104A ARG* 1.3 71.4 + - - +
105A LYS* 3.4 6.8 + - - +
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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