Contacts of the strand formed by residues 81 - 86 (chain D) 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 PRO 81 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52D SER 3.6 12.8 - - - +
53D GLY* 3.4 1.4 - - - -
54D ILE 2.9 23.9 + - - -
80D VAL* 1.3 92.3 - - + +
82D VAL* 1.3 60.3 + - - +
174D ARG* 3.4 44.4 - - + +
197D PHE* 3.7 20.2 - - + -
201D ILE* 3.6 31.9 - - + +
202D CYS* 3.8 8.1 - - - -
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Residues in contact with VAL 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D ILE* 3.2 16.6 - - + +
56D LEU* 4.1 12.6 - - + -
75D VAL* 3.4 47.1 - - + +
76D PHE* 4.7 1.8 - - + -
80D VAL 3.7 9.2 - - - +
81D PRO* 1.3 81.0 - - - +
83D PHE* 1.3 63.1 + - - +
84D GLY 4.2 0.2 - - - -
92D MET* 3.7 19.2 - - + +
174D ARG 3.0 7.7 + - - +
175D PHE* 3.4 22.6 - - + -
176D TYR* 2.9 26.9 + - - +
197D PHE* 3.9 2.5 - - - -
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Residues in contact with PHE 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D ILE 2.8 9.0 + - - +
55D ILE* 3.3 15.4 - - + +
56D LEU 2.9 23.8 + - - -
82D VAL* 1.3 75.4 - - - +
84D GLY* 1.3 62.9 + - - +
85D VAL* 4.6 8.5 - - + -
121D LEU* 3.9 22.4 - - + -
176D TYR* 3.4 16.8 - + + -
178D VAL* 3.5 41.5 - - + -
182D PRO* 4.3 15.0 - - + -
193D MET* 5.2 5.4 - - + -
194D LEU* 3.9 29.6 - - + -
197D PHE* 3.5 42.0 - + + -
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Residues in contact with GLY 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D LEU* 3.5 9.6 - - - -
83D PHE* 1.3 74.0 - - - +
85D VAL* 1.3 62.4 + - - -
88D GLY 3.8 17.3 - - - -
89D MET* 3.7 7.1 - - - +
92D MET* 4.1 5.9 - - - +
176D TYR 2.8 15.0 + - - -
177D GLY* 3.2 2.4 - - - -
178D VAL* 2.9 30.0 + - - +
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Residues in contact with VAL 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D VAL* 5.7 8.3 - - + -
55D ILE* 4.5 14.8 - - + -
56D LEU 2.8 17.9 + - - +
57D SER* 3.3 17.0 - - - +
58D GLY 5.0 1.6 - - - +
83D PHE* 4.6 9.0 - - + +
84D GLY* 1.3 75.5 - - - +
86D CYS* 1.3 66.6 + - - +
87D TYR 3.1 1.7 + - - -
88D GLY 2.9 17.5 + - - -
89D MET 3.8 0.6 - - - +
178D VAL* 3.8 6.5 - - + -
180D PHE 3.5 20.9 - - - +
181D HIS* 3.8 22.4 - - + +
182D PRO* 4.0 21.8 - - + -
183D GLU* 4.2 5.6 - - - +
194D LEU* 6.2 0.4 - - + -
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Residues in contact with CYS 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D GLY* 4.3 3.1 - - - -
85D VAL* 1.3 71.2 - - - +
87D TYR* 1.3 60.8 + - - +
89D MET* 2.7 25.8 + - - +
90D GLN* 2.9 18.6 + - - +
142D SER* 3.5 21.3 - - - +
178D VAL 2.8 17.6 + - - -
179D GLN* 4.1 13.8 - - - +
180D PHE 4.0 7.6 - - - -
181D HIS* 3.4 38.4 - - - -
529D CIT 3.4 20.0 - - - +
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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