Contacts of the strand formed by residues 63 - 69 (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 PHE 63 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32Y TRP* 3.3 54.5 - + + -
56Y PHE* 4.2 18.8 - + + -
58Y ASN* 3.9 22.9 - - + -
60Y SER 3.0 28.0 - - - -
61Y GLU* 3.5 23.8 - - + -
62Y SER* 1.3 76.5 - - - +
64Y VAL* 1.3 67.8 + - - +
65Y LEU* 4.3 1.6 + - + -
82Y PHE 4.8 1.0 - - - +
83Y PRO* 4.9 3.8 - - - +
125Y ALA* 5.0 0.2 - - + -
126Y ILE 3.1 16.2 - - - +
127Y SER* 4.2 9.4 - - - -
133Y GLN* 6.1 0.2 - - + -
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Residues in contact with VAL 64 (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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63Y PHE* 1.3 79.9 - - - +
65Y LEU* 1.3 60.8 + - - +
66Y ASN* 3.8 15.2 + - - +
81Y ALA* 6.2 0.2 - - + -
82Y PHE 3.6 12.6 - - - +
83Y PRO* 4.4 11.9 - - + -
124Y GLY 3.9 0.2 - - - +
125Y ALA* 3.8 1.4 - - - -
126Y ILE* 2.7 50.6 + - + +
128Y LEU* 3.6 33.0 - - + -
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Residues in contact with LEU 65 (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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35Y PRO* 4.9 1.1 - - + -
54Y CYS* 4.1 23.8 - - + -
56Y PHE* 4.4 19.7 - - + -
63Y PHE* 4.2 0.9 - - + -
64Y VAL* 1.3 70.4 - - - +
66Y ASN* 1.3 70.5 + - - +
81Y ALA* 3.2 2.1 - - - +
82Y PHE* 2.9 41.9 + - + +
97Y VAL* 4.9 6.5 - - + -
106Y PHE* 3.4 55.9 - - + -
108Y MET* 5.5 2.9 - - + -
123Y CYS* 5.2 1.1 - - + -
124Y GLY 3.4 23.1 - - - +
125Y ALA* 4.2 7.4 - - + +
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Residues in contact with ASN 66 (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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64Y VAL* 3.8 11.1 - - - +
65Y LEU* 1.3 92.5 - - - +
67Y TRP* 1.3 61.2 + - - +
68Y TYR* 2.7 37.6 + - + +
78Y LYS* 3.1 29.9 + - - +
80Y ALA 4.0 2.9 - - - +
81Y ALA* 3.6 9.2 - - - +
108Y MET* 4.4 4.1 - - - +
123Y CYS* 3.3 9.0 - - - +
124Y GLY 2.9 32.7 + - - +
126Y ILE* 3.2 22.7 - - + +
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Residues in contact with TRP 67 (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* 3.6 16.6 - - - -
52Y PHE* 4.2 14.1 - + - -
66Y ASN* 1.3 72.7 - - - +
68Y TYR* 1.3 79.7 + - - +
78Y LYS* 3.6 0.7 - - - -
79Y LEU* 3.0 31.3 + - + -
80Y ALA* 3.1 31.1 + - + +
95Y PHE* 3.6 28.9 - + + -
96Y ARG 3.9 4.0 - - - -
97Y VAL* 4.2 0.4 - - + -
108Y MET* 3.6 40.2 - - + -
109Y SER 3.2 47.8 - - - -
110Y VAL* 3.2 20.2 - - + -
121Y TYR* 4.1 14.5 - + - -
122Y LEU 3.1 19.4 + - - -
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Residues in contact with TYR 68 (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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66Y ASN* 2.7 46.5 + - + +
67Y TRP* 1.3 80.2 - - - +
69Y ARG* 1.3 61.7 + - - +
70Y MET* 5.7 0.2 - - + -
76Y THR* 3.3 37.0 - - + +
77Y ASP 3.6 1.6 - - - +
78Y LYS* 3.4 28.3 - - + -
79Y LEU* 3.3 8.5 - - - -
121Y TYR* 3.3 12.3 - - - -
122Y LEU* 3.0 67.1 + - + +
124Y GLY* 4.1 12.6 - - - -
126Y ILE* 3.5 11.6 - - - +
134Y ILE* 3.8 13.8 - - + +
136Y GLU* 5.8 0.9 - - + -
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Residues in contact with ARG 69 (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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68Y TYR* 1.3 75.8 - - - +
70Y MET* 1.3 76.9 + - - +
77Y ASP* 3.2 33.2 + - + +
79Y LEU* 3.3 17.6 - - + +
95Y PHE* 6.1 1.4 - - - -
116Y ASN* 2.5 34.1 + - - +
117Y ASP* 3.4 19.7 + - - +
118Y SER 3.0 21.8 + - - -
119Y GLY* 4.4 1.8 - - - -
120Y THR 3.3 15.0 - - - +
121Y TYR* 3.3 36.1 + - + -
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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