Contacts of the strand formed by residues 63 - 69 (chain B) in PDB entry 5GOW
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 ILE 63 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56B SER* 4.0 3.4 - - - +
57B PRO 5.4 1.8 - - - +
58B GLU* 4.4 6.5 - - + +
60B LYS 5.7 2.0 - - - +
61B ALA 5.8 0.2 - - - -
62B LYS* 1.3 81.2 - - - +
64B GLN* 1.3 63.9 + - - +
79B PHE* 2.7 34.5 + - + +
82B GLU* 6.3 1.3 - - - -
85B ALA* 3.5 29.6 - - + +
86B VAL* 3.3 31.0 - - + +
89B ARG* 3.3 49.1 - - + +
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Residues in contact with GLN 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397A ASP* 4.9 1.6 - - - +
398A GLU* 4.8 0.9 - - - +
399A GLU 2.8 30.7 + - - +
400A ASP* 3.1 23.2 + - - +
403A PHE* 3.3 17.1 - - + -
55B ILE* 3.3 3.8 - - - -
56B SER* 2.6 51.2 + - - +
60B LYS* 4.2 1.2 - - - +
62B LYS* 3.2 38.7 - - + +
63B ILE* 1.3 74.4 - - - +
65B LEU* 1.3 58.7 + - - +
76B ASN* 6.0 0.2 - - - -
77B PHE 3.3 6.1 - - - +
78B HIS* 3.9 19.6 + - - +
79B PHE* 4.1 1.6 - - - -
89B ARG* 3.3 11.8 - - - +
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Residues in contact with LEU 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403A PHE* 3.4 5.6 - - - -
53B GLN* 4.5 4.5 - - + +
54B LYS 3.1 12.6 - - - +
55B ILE* 3.4 27.8 - - + -
64B GLN* 1.3 72.4 - - - +
66B GLN* 1.3 59.0 + - - +
67B LEU* 5.1 5.4 - - + -
77B PHE* 2.6 47.3 + - + +
79B PHE* 3.4 15.0 - - + -
89B ARG* 3.3 32.8 - - + +
92B VAL* 3.3 34.1 - - + -
93B LYS* 3.9 5.2 - - + +
96B LEU* 3.8 16.4 - - + -
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Residues in contact with GLN 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400A ASP* 4.9 1.2 + - - +
403A PHE* 3.2 28.4 - - + +
53B GLN* 3.1 8.3 - - - +
54B LYS* 2.7 88.3 + - + +
65B LEU* 1.3 77.3 - - - +
67B LEU* 1.3 63.0 + - - +
68B VAL* 3.1 12.5 - - + +
74B THR* 3.6 13.5 - - - +
75B THR 3.2 5.2 - - - -
76B ASN* 3.0 33.0 + - - +
77B PHE* 5.1 0.2 - - - -
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Residues in contact with LEU 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B ILE* 3.4 38.4 - - + -
45B HIS* 4.0 9.0 - - + -
50B ILE* 3.9 27.1 - - + -
52B CYS 4.0 2.2 - - - -
53B GLN* 4.8 3.1 - - + -
65B LEU* 5.1 2.7 - - + -
66B GLN* 1.3 74.0 - - - +
68B VAL* 1.3 62.1 + - - +
69B LEU* 3.5 7.7 + - + +
74B THR* 3.0 5.6 - - - -
75B THR* 2.6 48.2 + - - +
77B PHE* 3.6 20.2 - - + -
96B LEU* 3.7 34.1 - - + -
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Residues in contact with VAL 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405A GLU* 3.3 20.6 - - - +
50B ILE 3.8 0.2 - - - -
51B LYS* 2.7 32.3 + - + +
52B CYS* 2.7 46.8 + - - +
54B LYS* 3.4 7.0 - - + +
66B GLN* 3.1 34.8 - - + +
67B LEU* 1.3 71.2 - - - +
69B LEU* 1.3 58.4 + - - +
74B THR* 3.5 18.2 - - + -
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Residues in contact with LEU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B HIS* 4.6 12.3 - - + +
49B ASP* 3.2 21.8 - - + +
50B ILE* 3.3 37.2 - - + -
51B LYS* 3.6 5.5 - - - +
67B LEU* 3.7 15.9 - - + +
68B VAL* 1.3 80.7 - - - +
70B HIS* 1.3 59.6 + - - +
71B ALA* 3.0 19.9 + - + +
72B GLY* 3.3 9.9 + - - -
73B ASP* 2.8 50.8 + - + +
75B THR* 4.2 7.6 - - - +
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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