Contacts of the strand formed by residues 86 - 90 (chain D) in PDB entry 1GMO
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 ALA 86 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50D LEU* 5.3 0.9 - - + -
74D CYS* 4.8 1.8 - - - -
84D CYS* 3.5 7.8 + - - -
85D LYS* 1.3 81.4 - - - +
87D PHE* 1.3 59.5 + - - +
99D PHE* 2.8 39.0 + - + +
101D PHE 3.3 16.2 - - - +
102D ASN* 4.1 10.8 - - + -
118D LEU* 4.3 7.9 - - + -
119D TYR 3.2 14.4 - - - +
120D GLU* 3.9 11.9 - - + -
121D ASN 4.2 0.4 - - - +
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Residues in contact with PHE 87 (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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39D ILE* 4.5 0.7 - - + -
42D PHE* 3.6 26.2 - + - -
67D ALA* 4.1 5.4 - - + -
70D CYS* 3.3 27.6 - - + -
71D ALA* 3.5 34.1 - - + -
74D CYS* 3.9 10.1 - - + -
84D CYS* 4.5 0.4 - - - -
86D ALA* 1.3 77.4 - - - +
88D VAL* 1.3 70.4 + - - +
89D PHE* 4.5 3.6 - - + -
96D CYS* 5.3 0.2 - - + -
97D LEU 3.2 9.0 - - - +
98D TRP* 3.6 22.9 - + + -
99D PHE* 4.2 0.7 - - - -
118D LEU* 4.2 0.2 - - - -
119D TYR* 2.9 79.2 + + + -
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Residues in contact with VAL 88 (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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48D THR 3.8 9.2 - - - +
49D THR* 3.8 27.8 - - - +
50D LEU 4.1 1.8 - - - +
87D PHE* 1.3 75.0 - - - +
89D PHE* 1.3 63.8 + - - +
96D CYS* 3.7 2.1 - - - -
97D LEU* 2.9 41.7 + - + +
99D PHE* 3.3 26.5 - - + -
116D PHE* 3.6 31.2 - - + -
117D ASP 3.7 4.9 - - - +
118D LEU* 3.6 23.3 - - + -
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Residues in contact with PHE 89 (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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64D VAL* 4.7 1.6 - - + -
65D ASN 3.6 20.4 - - - -
66D THR* 4.1 6.5 - - - -
67D ALA* 3.4 41.1 - - + -
70D CYS* 3.6 19.3 - - - -
87D PHE* 4.2 2.2 + - + -
88D VAL* 1.3 75.4 - - - +
90D ASP* 1.3 59.3 + - - +
91D LYS* 3.4 34.7 + - + -
94D LYS* 3.7 15.7 - - + -
95D GLN 3.4 31.9 - - - -
96D CYS* 5.1 0.4 - - - -
115D GLU 3.7 3.1 - - - +
116D PHE* 3.8 3.1 - - - -
117D ASP* 3.2 35.2 + - + +
119D TYR* 4.3 6.3 - - + -
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Residues in contact with ASP 90 (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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88D VAL 4.0 0.8 + - - -
89D PHE* 1.3 74.4 - - - +
91D LYS* 1.3 51.9 + - - +
92D ALA* 2.7 20.2 + - - +
93D ARG* 2.4 54.4 + - + +
94D LYS* 2.5 39.2 + - - -
95D GLN* 3.0 25.9 + - + +
97D LEU* 4.7 4.9 - - + -
115D GLU* 4.4 5.7 - - - +
116D PHE* 3.3 33.2 - - + -
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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
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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