Contacts of the helix formed by residues 69 - 91 (chain B) in PDB entry 2GTP
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 TYR 69 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B LYS* 4.2 14.7 - - - +
61B TYR* 4.0 24.6 + + - -
65B GLU* 3.6 18.2 - - + -
66B CYS 3.1 9.9 + - - +
68B GLN* 1.3 79.9 - - + +
70B LYS* 1.3 67.2 + - - +
71B ALA 3.3 2.7 - - - -
72B VAL* 2.9 27.8 + - + +
73B VAL* 3.0 13.1 + - + +
169B PRO* 4.2 4.9 - - + -
174B VAL* 3.8 42.2 - - + -
177B THR* 4.0 28.3 - - + -
179B VAL* 5.7 4.0 - - + -
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Residues in contact with LYS 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LYS* 3.1 23.5 + - + +
69B TYR* 1.3 76.9 - - - +
71B ALA* 1.3 64.6 + - - +
73B VAL* 3.0 11.8 + - - +
74B TYR* 3.0 40.2 + - + -
117B GLY* 3.2 29.2 + - - +
118B PHE* 4.4 13.2 - - - -
165B PRO 4.7 11.9 - - - -
167B TYR* 3.4 35.4 - - + +
169B PRO* 3.7 18.1 - - + +
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Residues in contact with ALA 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LYS 4.8 0.2 + - - -
68B GLN 4.5 7.5 + - - +
69B TYR 3.3 0.6 - - - -
70B LYS* 1.3 78.3 - - - +
72B VAL* 1.3 60.6 + - + +
74B TYR* 3.6 5.8 + - - +
75B SER* 2.9 29.5 + - - -
116B GLU* 4.3 15.6 - - + +
117B GLY* 3.8 28.8 - - - +
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Residues in contact with VAL 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B GLN 4.8 4.3 - - - +
69B TYR* 2.9 28.1 + - + +
71B ALA* 1.3 75.9 - - + +
73B VAL* 1.3 60.9 + - - +
75B SER* 3.6 5.7 - - - -
76B ASN* 2.8 32.5 + - - +
177B THR* 3.8 27.1 - - + -
178B ARG 4.0 7.6 - - - +
179B VAL* 3.9 26.0 - - + -
171C LYS* 6.1 5.2 - - + +
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Residues in contact with VAL 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B TYR* 3.0 12.4 + - + +
70B LYS 3.0 9.0 + - - +
72B VAL* 1.3 75.8 - - - +
74B TYR* 1.3 59.1 + - - +
76B ASN* 3.2 6.4 + - - +
77B THR* 2.8 35.8 + - - +
155B TYR* 3.3 48.0 - - + +
162B ILE* 3.7 26.5 - - + -
167B TYR* 3.8 21.1 - - + +
169B PRO* 4.9 1.8 - - + -
173B ASP* 4.0 6.7 - - + +
177B THR* 3.7 11.4 - - + -
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Residues in contact with TYR 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B LYS* 3.0 33.8 + - + -
71B ALA* 3.9 5.8 - - - +
73B VAL* 1.3 74.6 - - + +
75B SER* 1.3 58.6 + - - +
77B THR* 3.2 3.4 + - - -
78B ILE* 2.8 42.4 + - + +
117B GLY* 3.8 12.3 - - - +
118B PHE* 3.7 32.3 - - - +
119B MET* 3.5 49.0 + - + +
162B ILE* 3.2 46.2 + - + -
163B ALA* 4.6 2.5 + - - -
164B GLN 4.2 5.5 + - - -
165B PRO 5.4 0.2 + - - -
167B TYR* 3.7 14.6 - + - +
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Residues in contact with SER 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ALA 2.9 19.7 + - - -
72B VAL* 3.6 7.9 - - - -
74B TYR* 1.3 77.8 - - - +
76B ASN* 1.3 59.6 + - - +
78B ILE* 4.0 6.4 - - - +
79B GLN* 2.9 33.6 + - - +
171C LYS* 5.6 5.5 - - - +
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Residues in contact with ASN 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B VAL* 2.8 25.4 + - - +
73B VAL 3.5 4.7 - - - +
75B SER* 1.3 74.0 + - - +
77B THR* 1.3 59.5 + - - +
79B GLN* 3.9 3.1 - - - +
80B SER* 2.9 35.0 + - - -
149B ASN* 5.1 9.4 - - + +
151B SER* 5.6 0.6 - - - -
155B TYR* 4.0 19.5 - - + -
176B ARG 4.3 0.2 - - - +
177B THR* 3.3 12.5 - - - +
178B ARG* 2.7 55.4 + - - +
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Residues in contact with THR 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B VAL* 2.8 26.0 + - - +
74B TYR* 3.6 6.9 - - - -
76B ASN* 1.3 71.9 - - - +
78B ILE* 1.3 65.5 + - - +
80B SER* 3.1 7.2 + - - -
81B ILE* 3.1 22.9 + - - +
119B MET* 4.7 6.3 - - + -
127B ILE* 4.6 7.9 - - + -
152B ALA* 6.3 0.2 - - - +
155B TYR* 3.5 25.7 - - + +
156B LEU* 3.5 27.1 - - + +
159B LEU* 3.8 20.6 - - + -
162B ILE* 4.9 4.7 - - + +
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Residues in contact with ILE 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B TYR* 2.8 29.8 + - + +
75B SER* 4.0 5.8 - - - +
77B THR* 1.3 75.4 - - - +
79B GLN* 1.3 64.2 + - - +
81B ILE* 3.4 9.7 - - - +
82B ILE* 3.1 30.5 + - + +
107B LEU* 5.3 4.0 - - + -
111B ALA* 4.0 28.3 - - + -
118B PHE 5.7 3.6 - - - +
119B MET* 3.8 23.6 - - + -
123B LEU* 4.2 17.0 - - + -
127B ILE* 4.2 9.0 - - + -
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Residues in contact with GLN 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B SER* 2.9 20.1 + - - +
76B ASN* 4.1 4.3 - - - +
78B ILE* 1.3 79.4 - - + +
80B SER* 1.3 56.7 + - - +
82B ILE* 3.8 10.5 - - - +
83B ALA* 3.1 27.4 + - - +
149B ASN* 4.9 7.4 - - - +
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Residues in contact with SER 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ASN* 2.9 21.3 + - - +
77B THR* 3.1 6.5 + - - -
79B GLN* 1.3 74.7 - - - +
81B ILE* 1.3 66.4 + - - +
83B ALA 3.2 1.7 + - - -
84B ILE* 3.2 26.7 + - - +
148B LEU* 3.5 10.0 - - - +
149B ASN* 3.5 23.7 + - - +
152B ALA* 3.5 35.0 - - - +
156B LEU* 4.5 4.0 - - - -
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Residues in contact with ILE 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B THR 3.1 12.1 + - - +
78B ILE* 3.4 12.6 - - - +
80B SER* 1.3 76.0 - - - +
82B ILE* 1.3 66.0 + - - +
84B ILE* 3.2 15.3 + - + +
85B ILE* 3.0 35.3 + - + +
107B LEU* 3.8 25.1 - - + -
127B ILE* 4.1 24.0 - - + -
130B LEU* 4.4 16.8 - - + -
131B TRP* 4.5 9.6 - - + +
136B VAL* 3.9 28.3 - - + -
156B LEU* 4.4 12.2 - - + +
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Residues in contact with ILE 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ILE* 3.1 27.3 + - + +
79B GLN* 3.8 7.9 - - - +
81B ILE* 1.3 77.7 - - - +
83B ALA* 1.3 59.6 + - - +
85B ILE* 3.2 3.0 + - - +
86B ARG* 2.9 66.0 + - - +
107B LEU* 3.8 24.0 - - + -
108B PHE* 3.9 21.0 - - + -
111B ALA* 4.0 25.4 - - + -
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Residues in contact with ALA 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B GLN 3.1 18.6 + - - +
80B SER 3.2 4.9 + - - +
82B ILE* 1.3 80.2 - - + +
84B ILE* 1.3 60.9 + - - +
86B ARG* 3.9 7.7 - - - +
87B ALA* 3.1 24.6 + - - +
146B TYR* 4.0 7.5 - - + +
147B GLN 3.9 21.3 - - - +
148B LEU* 4.2 8.1 - - + -
149B ASN* 5.6 2.0 - - - +
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Residues in contact with ILE 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B SER 3.2 15.9 + - - +
81B ILE* 3.2 19.5 + - + +
83B ALA* 1.3 74.4 - - - +
85B ILE* 1.3 62.1 + - - +
87B ALA 3.5 1.0 + - - -
88B MET* 3.2 22.1 + - + +
131B TRP* 3.9 28.7 - - + -
136B VAL* 3.5 37.0 - - + +
139B CYS* 3.5 14.4 - - + -
140B PHE* 4.1 14.8 - - + +
146B TYR* 4.0 14.1 - - - +
148B LEU* 3.8 16.8 - - + -
152B ALA* 5.3 0.7 - - + -
156B LEU* 4.2 7.2 - - + -
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Residues in contact with ILE 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B ILE* 3.0 23.4 + - + +
82B ILE 3.7 3.6 - - - +
84B ILE* 1.3 75.7 - - + +
86B ARG* 1.3 64.9 + - - +
88B MET* 3.2 25.2 + - + +
89B GLY* 3.5 4.2 + - - -
95B PHE* 4.9 9.6 - - + -
104B ALA* 4.2 15.9 - - + -
107B LEU* 3.2 32.1 - - + -
108B PHE* 3.8 23.8 - - + -
130B LEU* 3.3 33.2 - - + -
136B VAL* 5.0 3.4 - - + -
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Residues in contact with ARG 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B ILE* 2.9 46.3 + - - +
83B ALA* 3.9 7.3 - - - +
85B ILE* 1.3 72.9 - - - +
87B ALA* 1.3 63.1 + - - +
89B GLY* 3.1 12.7 + - - -
90B ARG* 3.2 15.0 + - - +
108B PHE* 4.0 26.4 - - + -
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Residues in contact with ALA 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B ALA 3.1 18.6 + - - +
84B ILE 3.6 6.1 - - - +
85B ILE 3.2 0.2 - - - -
86B ARG* 1.3 77.7 - - - +
88B MET* 1.3 53.0 + - - +
90B ARG* 3.1 10.7 + - - +
91B LEU* 2.7 40.6 + - + +
139B CYS* 3.7 5.8 - - - -
146B TYR* 3.5 42.6 - - + -
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Residues in contact with MET 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B ILE 3.2 14.3 + - - +
85B ILE* 3.2 15.0 + - + +
87B ALA* 1.3 78.1 - - - +
89B GLY* 1.3 56.4 + - - +
92B LYS* 2.8 25.1 + - - -
93B ILE* 2.9 45.5 + - + +
94B ASP 3.4 22.0 - - - +
95B PHE* 3.7 36.1 - - + -
135B GLY 3.7 15.7 - - - +
136B VAL* 3.8 20.6 - - - -
139B CYS* 3.6 17.5 - - + -
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Residues in contact with GLY 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ILE 3.5 4.8 + - - -
86B ARG* 3.1 8.1 + - - -
88B MET* 1.3 79.0 - - - +
90B ARG* 1.3 61.9 + - - +
92B LYS* 3.4 13.4 + - - +
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Residues in contact with ARG 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ARG 3.2 12.4 + - - +
87B ALA* 3.1 13.8 + - - +
89B GLY* 1.3 78.7 - - - +
91B LEU* 1.3 79.2 + - - +
92B LYS* 3.5 7.3 + - - +
145B GLU* 3.7 24.2 + - - +
146B TYR* 3.9 16.0 - - - +
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Residues in contact with LEU 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ALA* 2.7 23.7 + - + +
90B ARG* 1.3 98.6 - - - +
92B LYS* 1.3 71.5 + - - +
93B ILE* 3.4 12.4 + - + +
139B CYS* 4.1 20.9 - - - -
142B ARG* 3.8 34.0 + - + +
145B GLU* 3.4 31.6 - - + +
146B TYR* 4.4 14.8 - - + -
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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
------------------------------------------------------------
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