Contacts of the helix formed by residues 86 - 96 (chain B) in PDB entry 1GPM
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 CYS 86 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B VAL* 1.3 69.9 - - + +
87B TYR* 1.3 58.7 + - - +
89B MET* 2.5 28.3 + - - +
90B GLN* 2.9 19.3 + - - +
142B SER* 3.4 26.7 - - - +
178B VAL 2.8 20.3 + - - -
179B GLN* 3.7 20.9 - - - +
180B PHE 3.7 9.4 - - - -
181B HIS* 3.6 31.0 - - + -
529B CIT 3.3 16.6 - - - +
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Residues in contact with TYR 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B PHE* 3.7 30.3 - + + -
58B GLY 3.6 1.6 - - - -
59B GLY* 3.1 33.9 - - - +
61B GLU* 3.0 36.3 - - + -
63B THR* 3.4 19.7 - - + +
68B SER* 3.7 4.7 - - - -
69B PRO* 2.6 43.4 + - + +
70B ARG* 3.2 11.4 + - - -
85B VAL 2.9 1.4 + - - -
86B CYS* 1.3 77.2 - - - +
88B GLY* 1.3 58.8 + - - +
90B GLN* 3.0 16.0 + - - +
91B THR* 2.8 42.6 + - + -
529B CIT 3.3 8.2 + - - +
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Residues in contact with GLY 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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15B PHE* 4.8 0.7 - - - -
56B LEU* 3.7 25.8 - - - +
57B SER 2.7 23.7 + - - -
84B GLY* 3.7 8.6 - - - -
85B VAL 3.1 0.6 + - - -
86B CYS 3.0 1.0 - - - -
87B TYR* 1.3 75.3 - - - +
89B MET* 1.3 57.3 + - - +
91B THR* 3.4 9.9 - - - +
92B MET* 3.1 28.1 + - - +
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Residues in contact with MET 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B GLY* 3.7 15.0 - - - +
86B CYS* 2.5 18.6 + - - +
88B GLY* 1.3 71.2 - - - -
90B GLN* 1.3 64.0 + - - -
92B MET* 3.3 7.1 + - - +
93B ALA 3.1 17.7 + - - -
147B VAL* 4.0 7.9 - - + -
165B PHE* 3.1 38.4 - - + +
166B ALA 4.6 0.7 - - - -
168B MET* 3.3 43.3 - - + +
177B GLY* 3.4 28.5 - - - +
178B VAL 3.3 15.9 - - - +
179B GLN* 3.5 26.9 - - + +
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Residues in contact with GLN 90 (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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61B GLU 5.2 1.0 - - - +
63B THR* 4.1 17.9 + - + +
86B CYS 2.9 16.2 + - - +
87B TYR* 3.5 19.9 - - - +
89B MET* 1.3 79.1 - - - +
91B THR* 1.3 62.2 + - - +
93B ALA* 3.1 8.2 + - - +
94B MET* 3.0 24.5 + - - +
100B VAL* 4.2 3.4 - - + +
142B SER 5.1 0.6 + - - -
143B HIS* 4.4 3.0 - - - +
144B GLY 4.0 14.3 - - - +
145B ASP* 3.6 38.5 + - + +
147B VAL* 3.8 21.3 - - + -
179B GLN* 3.7 19.3 + - - +
529B CIT 4.5 8.4 + - - +
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Residues in contact with THR 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B PHE* 4.3 18.6 - - + -
56B LEU* 4.5 3.6 - - + -
63B THR* 3.8 8.4 - - - +
69B PRO 3.7 7.6 + - - -
70B ARG* 3.4 17.7 + - - -
71B ALA* 4.5 5.6 - - + -
87B TYR* 2.8 30.2 + - + +
88B GLY* 3.4 17.7 - - - +
90B GLN* 1.3 73.0 - - - +
92B MET* 1.3 66.4 + - - +
94B MET* 3.3 3.2 + - - +
95B GLN* 3.0 53.0 + - - +
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Residues in contact with MET 92 (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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56B LEU* 4.6 3.1 - - + -
76B PHE* 3.6 38.8 - - + -
82B VAL* 3.8 24.7 - - + +
84B GLY 4.7 2.9 - - - +
88B GLY 3.1 15.5 + - - +
89B MET 3.4 6.5 - - - +
90B GLN 3.2 0.2 - - - -
91B THR* 1.3 81.0 - - - +
93B ALA* 1.3 62.3 + - - +
95B GLN* 4.4 0.2 - - - -
96B LEU* 3.3 34.5 + - + +
151B PRO* 4.2 0.5 - - - +
154B PHE* 4.2 20.4 - - + -
168B MET* 5.2 2.5 - - + +
175B PHE* 3.8 22.0 - - + -
176B TYR 3.8 25.6 - - - +
177B GLY* 4.6 5.6 - - - -
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Residues in contact with ALA 93 (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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89B MET 3.1 5.3 + - - +
90B GLN* 3.1 10.9 + - - +
92B MET* 1.3 75.1 - - - +
94B MET* 1.3 63.8 + - - +
96B LEU 3.2 1.2 + - - -
97B GLY 3.1 5.7 + - - -
98B GLY* 2.7 34.3 + - - -
100B VAL* 4.6 5.2 - - + -
147B VAL* 4.5 15.7 - - + -
149B ALA 4.5 0.2 - - - +
151B PRO* 3.6 18.2 - - + +
168B MET* 3.7 23.8 - - + +
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Residues in contact with MET 94 (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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63B THR* 3.8 36.8 - - + +
64B THR* 5.5 2.0 - - - -
70B ARG* 4.5 16.2 - - - +
90B GLN 3.0 16.0 + - - +
91B THR* 3.5 9.2 - - - +
93B ALA* 1.3 78.4 - - - +
95B GLN* 1.3 59.6 + - + +
96B LEU 2.9 6.8 + - - -
97B GLY* 3.3 7.6 + - - -
98B GLY 3.4 21.7 - - - +
99B HIS* 3.7 5.2 - - + -
100B VAL* 3.4 38.6 - - + +
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Residues in contact with GLN 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ARG* 3.5 20.9 - - + +
71B ALA* 2.7 50.6 + - - +
73B GLN* 2.7 36.8 + - - +
76B PHE* 3.1 26.1 - - + -
91B THR* 3.0 27.1 + - - +
92B MET 4.5 0.4 - - - +
94B MET* 1.3 76.7 - - - +
96B LEU* 1.3 66.3 + - - +
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Residues in contact with LEU 96 (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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73B GLN* 5.2 2.2 - - - +
76B PHE* 4.0 35.7 - - + -
92B MET* 3.3 30.0 + - + +
93B ALA 3.2 1.9 + - - -
94B MET 2.9 1.2 + - - -
95B GLN* 1.3 87.1 - - - +
97B GLY* 1.3 58.8 + - - +
98B GLY 3.8 0.4 - - - -
151B PRO* 3.5 21.9 - - + +
152B SER* 5.0 2.1 + - - -
154B PHE* 3.9 25.8 - - + -
173B LYS* 5.2 10.3 - - - +
175B PHE* 4.1 11.9 - - + -
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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