Contacts of the strand formed by residues 105 - 110 (chain Y) in PDB entry 5GGR
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 105 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53Y THR* 4.1 19.5 - - + +
54Y CYS 3.7 4.5 - - - -
55Y SER* 3.0 16.9 - - - +
99Y GLN* 4.1 0.9 - - - +
100Y LEU* 3.0 38.2 + - + +
102Y ASN* 3.0 21.8 + - - +
104Y ARG* 1.3 98.6 + - - +
106Y PHE* 1.3 61.3 + - - +
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Residues in contact with PHE 106 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53Y THR* 3.3 7.4 - - - +
54Y CYS* 2.6 46.0 + - + +
56Y PHE* 3.4 15.9 - + - -
65Y LEU* 3.4 31.6 - - + -
82Y PHE* 3.6 24.7 - + - -
97Y VAL* 4.6 10.5 - - + -
98Y THR 3.5 5.4 - - - +
99Y GLN* 3.4 47.6 - - + -
103Y GLY 5.1 0.7 - - - -
104Y ARG* 2.9 33.2 - - - -
105Y ASP* 1.3 75.3 - - - +
107Y HIS* 1.3 64.3 + - - +
108Y MET* 3.8 1.5 + - + -
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Residues in contact with HIS 107 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51Y THR* 4.3 16.4 - - + +
52Y PHE 3.7 0.4 - - - -
53Y THR* 4.0 20.9 + - + +
96Y ARG 3.3 9.4 - - - +
97Y VAL* 3.3 2.5 - - - -
98Y THR* 2.7 46.5 + - - +
100Y LEU* 3.3 42.3 - - + +
106Y PHE* 1.3 75.4 - - - +
108Y MET* 1.3 61.1 + - - +
109Y SER* 3.8 8.5 + - - +
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Residues in contact with MET 108 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37Y PHE* 3.4 28.0 - - + -
51Y THR* 3.3 0.2 - - - -
52Y PHE* 2.6 55.8 + - + +
54Y CYS* 3.9 17.3 - - + +
65Y LEU* 5.5 4.0 - - + -
66Y ASN* 4.4 6.5 - - - +
67Y TRP* 3.6 45.4 - - + +
96Y ARG 3.9 3.1 - - - -
97Y VAL* 3.6 42.0 - - + -
106Y PHE* 4.3 1.6 - - + +
107Y HIS* 1.3 71.6 - - - +
109Y SER* 1.3 59.5 + - - +
123Y CYS* 3.7 12.6 - - + -
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Residues in contact with SER 109 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49Y ASN* 6.4 0.4 - - - -
50Y ALA 3.4 4.7 - - - -
51Y THR* 2.6 31.5 + - - +
67Y TRP* 3.2 8.3 - - - -
94Y ARG 3.2 7.1 - - - +
96Y ARG* 3.1 38.6 + - - +
107Y HIS* 4.3 7.3 + - - +
108Y MET* 1.3 77.1 + - - +
110Y VAL* 1.3 61.8 + - - +
111Y VAL* 4.7 8.5 - - - +
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Residues in contact with VAL 110 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48Y ASP 4.5 0.2 - - - +
49Y ASN* 3.6 1.4 - - - -
50Y ALA* 2.9 41.3 + - + +
52Y PHE* 6.3 0.2 - - + -
67Y TRP* 3.2 25.3 - - + -
94Y ARG* 4.0 4.0 - - - +
95Y PHE* 3.4 33.7 - - + -
109Y SER* 1.3 72.6 - - - +
111Y VAL* 1.3 75.2 + - - +
113Y ALA* 4.3 10.1 - - + -
117Y ASP* 4.0 18.8 - - + +
121Y TYR* 4.4 17.3 - - + +
142Y LEU* 4.9 6.1 - - + -
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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