Contacts of the strand formed by residues 68 - 73 (chain A) 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 PHE 68 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A VAL* 4.2 9.2 - - + -
60A TYR* 3.2 17.7 - - + -
64A VAL* 3.0 46.9 + - + +
66A GLY* 4.5 3.6 + - - -
67A ARG* 1.3 115.0 + - + +
69A THR* 1.3 68.0 + - - +
81A LEU* 4.3 11.7 - - + -
82A GLN 3.1 7.0 - - - +
83A MET* 3.9 21.1 - - + -
84A ASN 4.5 1.3 - - - -
86A LEU* 4.1 17.0 - - + -
90A ASP* 3.6 16.8 - - - -
94A TYR* 3.8 31.4 - + - -
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Residues in contact with THR 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ARG* 5.6 3.6 - - - +
60A TYR* 3.2 14.1 - - - +
67A ARG 4.1 4.5 + - - -
68A PHE* 1.3 79.7 + - - +
70A ILE* 1.3 65.8 + - - +
71A SER* 5.4 5.2 + - - -
80A PHE 4.1 0.5 - - - +
81A LEU* 3.5 5.7 - - - +
82A GLN* 2.6 54.5 + - - +
84A ASN* 4.6 2.4 + - - -
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Residues in contact with ILE 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A MET 4.5 2.5 - - - +
35A HIS 5.0 0.2 - - - -
36A TRP* 3.6 29.4 - - + +
49A ALA* 3.9 12.6 - - + +
50A VAL* 3.5 44.0 - - - +
51A ILE* 3.5 19.1 - - + +
58A ARG* 3.3 22.1 + - + -
60A TYR* 2.5 40.5 + - + +
69A THR* 1.3 75.7 - - - +
71A SER* 1.3 66.6 + - - +
79A LEU* 4.2 4.3 - - + -
80A PHE 3.8 6.3 - - - +
81A LEU* 4.4 5.2 - - + -
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Residues in contact with SER 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A ILE* 3.5 12.1 - - - -
58A ARG* 4.0 11.9 - - - -
69A THR* 4.1 5.0 + - - -
70A ILE* 1.3 76.9 - - - +
72A ARG* 1.3 65.2 + - - +
79A LEU* 3.5 6.4 - - - +
80A PHE* 2.8 46.0 + - - +
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Residues in contact with ARG 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A PHE* 2.6 66.0 + - + -
30A SER 3.7 5.3 + - - -
32A SER 2.9 18.6 + - - -
34A MET* 3.4 23.6 - - - +
51A ILE* 3.5 20.3 + - + +
52A TRP 3.6 13.1 + - - -
53A TYR* 3.0 27.9 + - - +
54A ASP 5.2 5.8 - - - +
55A GLY* 4.9 0.4 - - - +
58A ARG* 5.5 0.2 - - - +
71A SER* 1.3 80.0 + - - +
73A ASP* 1.3 60.8 + - - +
74A ASN* 2.6 21.5 + - - +
78A THR 3.6 4.9 - - - +
79A LEU* 4.5 4.3 - - + -
80A PHE* 4.4 3.4 - - - -
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Residues in contact with ASP 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A PHE* 4.1 0.6 - - - -
72A ARG* 1.3 73.6 - - - +
74A ASN* 1.3 56.8 + - - +
75A SER* 3.1 27.2 + - - -
76A LYS* 2.8 30.3 + - + +
77A ASN 3.1 6.6 + - - -
78A THR 3.0 30.0 + - - -
80A PHE* 3.5 23.1 - - + -
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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