Contacts of the strand formed by residues 50 - 56 (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 50 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31B ILE* 4.3 2.9 - - + -
45B HIS* 3.7 22.2 - - + -
46B MET 3.0 21.1 - - - +
47B TYR* 3.3 7.8 + - + +
49B ASP* 1.3 79.3 - - + +
51B LYS* 1.3 58.5 + - - +
52B CYS 3.4 22.4 - - - +
67B LEU* 3.9 24.5 - - + -
68B VAL 3.8 2.9 - - - +
69B LEU* 3.3 23.6 - - + -
70B HIS* 3.4 5.7 - - - -
100B LEU* 3.3 37.0 - - + -
104B LYS* 3.1 22.9 - - - +
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Residues in contact with LYS 51 (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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409A ASP* 2.6 34.2 + - - +
410A ASP* 2.6 56.6 + - + +
50B ILE* 1.3 72.6 - - - +
52B CYS* 1.3 76.5 + - - +
68B VAL* 2.7 17.5 + - + +
69B LEU* 3.6 7.5 - - - +
70B HIS* 3.4 36.9 + - + +
100B LEU* 5.3 0.2 - - - -
104B LYS* 2.7 32.5 + - - -
107B ALA* 5.6 1.2 - - - +
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Residues in contact with CYS 52 (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* 3.2 24.2 - - - +
407A ASP* 3.3 25.1 - - + -
408A GLU 3.5 10.8 - - - +
50B ILE* 3.4 11.8 - - - +
51B LYS* 1.3 96.1 - - - +
53B GLN* 1.3 61.7 + - - +
68B VAL* 2.7 58.8 + - - +
100B LEU* 4.5 1.3 - - - -
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Residues in contact with GLN 53 (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* 3.1 14.9 - - - +
406A ASN* 3.4 15.5 + - + +
407A ASP* 2.7 27.8 + - + +
52B CYS* 1.3 79.2 - - - +
54B LYS* 1.3 65.2 + - - +
55B ILE* 5.1 1.3 - - + -
65B LEU* 4.5 4.3 - - + +
66B GLN 3.1 11.9 - - - +
67B LEU* 4.8 7.4 - - + -
68B VAL* 4.3 0.7 - - - -
93B LYS* 3.0 35.3 - - + +
96B LEU* 3.2 19.5 - - + +
97B GLN* 3.1 36.7 - - + +
100B LEU* 3.6 7.1 - - + +
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Residues in contact with LYS 54 (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* 3.2 47.1 - - + +
404A ASN 3.1 7.2 - - - +
405A GLU* 2.6 47.1 + - + +
53B GLN* 1.3 71.9 - - - +
55B ILE* 1.3 63.9 + - - +
65B LEU* 3.1 9.5 - - - +
66B GLN* 2.7 64.5 + - + +
68B VAL* 3.4 9.7 - - - +
74B THR* 5.2 0.2 - - - +
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Residues in contact with ILE 55 (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* 3.6 2.9 - - - -
404A ASN* 2.7 37.7 + - + +
406A ASN* 5.3 9.0 - - + +
53B GLN* 5.0 5.4 - - + +
54B LYS* 1.3 78.9 - - - +
56B SER* 1.3 59.4 + - - +
57B PRO* 3.3 8.6 - - + +
64B GLN 3.3 4.3 - - - -
65B LEU* 3.4 18.2 - - + -
89B ARG* 3.3 41.1 - - + +
90B ASP* 4.7 4.5 - - - +
93B LYS* 3.7 34.1 - - + -
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Residues in contact with SER 56 (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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402A ASP* 3.7 15.7 - - - -
403A PHE* 3.4 13.0 - - - +
55B ILE* 1.3 70.8 - - - +
57B PRO* 1.3 65.7 - - - +
60B LYS* 4.1 2.8 - - - +
62B LYS 3.7 7.6 + - - -
63B ILE* 3.6 2.6 - - - -
64B GLN* 2.6 69.3 + - - +
89B ARG* 3.2 17.8 + - - -
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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