Contacts of the strand formed by residues 63 - 69 (chain Z) 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 Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32Z TRP* 3.6 33.9 - + - -
56Z PHE* 3.3 33.4 - + + -
58Z ASN* 3.7 27.6 - - + -
60Z SER* 4.2 4.7 - - - -
61Z GLU* 2.9 33.4 - - + -
62Z SER* 1.3 81.5 - - - +
64Z VAL* 1.3 70.0 + - - +
65Z LEU* 4.3 2.0 - - + -
82Z PHE* 4.4 3.8 - - - +
83Z PRO* 5.0 2.6 - - - +
125Z ALA* 4.6 1.1 - - + -
126Z ILE 3.2 15.0 - - - +
127Z SER* 3.4 34.1 - - - -
128Z LEU* 5.1 2.3 - - - +
133Z GLN* 5.9 1.3 - - - -
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Residues in contact with VAL 64 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63Z PHE* 1.3 80.3 - - - +
65Z LEU* 1.3 62.6 + - - +
66Z ASN* 3.3 16.5 + - - +
81Z ALA* 5.5 1.8 - - + -
82Z PHE 3.4 16.2 - - - +
83Z PRO* 4.0 12.1 - - + -
124Z GLY 3.7 0.3 - - - +
125Z ALA* 3.5 1.9 - - - -
126Z ILE* 2.9 52.7 + - + +
128Z LEU* 4.2 27.4 - - + -
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Residues in contact with LEU 65 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35Z PRO* 5.0 4.7 - - + -
54Z CYS* 5.2 9.6 - - - -
56Z PHE* 3.9 26.9 - - + -
63Z PHE* 5.7 1.3 - - + -
64Z VAL* 1.3 70.1 - - - +
66Z ASN* 1.3 62.6 + - - +
81Z ALA* 3.1 4.2 - - - -
82Z PHE* 2.8 44.8 + - + +
97Z VAL* 4.6 3.2 - - + +
106Z PHE* 3.3 55.0 - - + -
108Z MET* 4.7 11.4 - - + -
123Z CYS* 5.5 0.9 - - - -
124Z GLY 4.5 2.2 - - - +
125Z ALA* 3.6 31.0 - - + +
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Residues in contact with ASN 66 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64Z VAL* 3.3 21.0 - - - +
65Z LEU* 1.3 80.9 - - - +
67Z TRP* 1.3 62.2 + - - +
68Z TYR* 3.3 30.8 + - + +
78Z LYS* 3.2 31.7 - - - +
80Z ALA 3.6 4.9 - - - +
81Z ALA* 3.4 12.0 - - - +
108Z MET* 4.0 1.3 - - - +
123Z CYS* 3.1 9.0 - - - +
124Z GLY 3.0 34.6 + - - +
126Z ILE* 4.1 12.9 - - - +
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Residues in contact with TRP 67 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37Z PHE* 3.5 20.1 - + - -
52Z PHE* 4.3 19.5 - + - -
66Z ASN* 1.3 76.3 - - - +
68Z TYR* 1.3 67.4 + - - +
79Z LEU* 2.9 40.7 + - + +
80Z ALA* 3.0 15.9 + - + +
95Z PHE* 4.6 4.3 - + + -
96Z ARG 4.0 12.8 - - - -
97Z VAL* 4.8 3.4 - - + -
108Z MET* 3.5 32.1 - - + -
109Z SER* 3.1 52.3 - - - -
110Z VAL* 3.4 19.5 - - + -
121Z TYR* 3.5 25.7 - + - +
122Z LEU 3.0 28.9 - - - -
123Z CYS* 4.3 0.2 - - - +
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Residues in contact with TYR 68 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66Z ASN* 3.3 42.9 + - + +
67Z TRP* 1.3 85.7 - - - +
69Z ARG* 1.3 62.1 + - - +
76Z THR* 3.4 38.6 - - + -
77Z ASP 3.2 9.4 - - - +
78Z LYS* 3.9 20.9 - - + -
79Z LEU* 3.4 5.8 - - - +
121Z TYR* 3.3 18.9 - - - -
122Z LEU* 2.8 45.8 + - + -
124Z GLY* 4.8 7.0 + - - -
126Z ILE* 3.7 16.5 - - - +
134Z ILE* 4.0 15.2 - - + +
136Z GLU* 5.2 4.9 - - + -
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Residues in contact with ARG 69 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68Z TYR* 1.3 76.2 - - - +
70Z MET* 1.3 86.3 + - - +
76Z THR* 3.3 7.6 - - - -
77Z ASP* 3.1 36.2 + - + +
79Z LEU* 3.7 13.9 - - + -
95Z PHE* 5.9 3.0 - - - -
114Z ARG* 5.6 0.2 - - - +
116Z ASN* 2.6 31.1 + - - -
117Z ASP* 3.3 27.1 + - - +
118Z SER 3.8 9.7 + - - -
119Z GLY* 4.9 2.6 - - - -
120Z THR 3.4 15.5 - - - +
121Z TYR* 3.3 29.3 + - + -
122Z LEU* 5.7 0.2 - - - -
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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