Contacts of the strand formed by residues 60 - 65 (chain W) in PDB entry 5GAG
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 VAL 60 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1W MET* 3.4 20.8 - - + +
2W PHE 5.2 0.7 + - - -
59W GLU* 1.3 76.6 - - - +
61W LEU* 1.3 76.4 + - - +
71W LYS* 3.6 35.0 - - + -
72W VAL 3.2 10.3 - - - +
73W LYS* 3.7 21.8 - - + -
94W ALA* 4.2 9.9 - - + -
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Residues in contact with LEU 61 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1W MET* 4.6 0.4 - - - -
2W PHE* 3.6 40.8 - - + +
4W ILE* 3.7 19.7 - - + -
50W MET* 4.2 3.4 - - + -
56W PHE* 3.4 48.0 - - + +
59W GLU* 3.7 15.5 - - + +
60W VAL* 1.3 83.6 - - - +
62W THR* 1.3 67.3 + - - +
71W LYS* 3.3 6.9 - - - +
72W VAL* 2.8 43.0 + - + +
74W ALA 5.4 2.2 - - - +
91W PHE* 4.6 8.3 - - + -
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Residues in contact with THR 62 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1W MET* 4.0 19.8 - - + +
2W PHE 3.4 12.0 + - - -
3W THR* 3.5 17.2 + - - +
4W ILE* 3.0 24.9 + - - +
61W LEU* 1.3 80.9 - - - +
63W ILE* 1.3 64.0 + - - +
64W VAL* 3.9 0.4 + - - -
69W GLU* 3.8 31.2 - - + +
70W ILE 3.5 4.0 - - - +
71W LYS* 3.7 25.1 - - + -
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Residues in contact with ILE 63 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4W ILE* 3.4 22.9 - - + +
6W ALA* 3.9 19.7 - - + -
30W ILE* 3.6 25.4 - - + -
40W ILE* 4.1 7.0 - - + -
42W LEU* 4.9 1.1 - - + -
61W LEU* 5.3 0.2 - - + -
62W THR* 1.3 75.7 - - - +
64W VAL* 1.3 61.3 + - - +
65W VAL* 3.6 21.4 + - + +
68W LYS 3.0 5.9 - - - +
69W GLU* 3.2 1.8 - - - -
70W ILE* 2.9 32.6 + - + +
72W VAL* 3.6 33.4 - - + -
91W PHE* 3.8 22.0 - - + -
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Residues in contact with VAL 64 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3W THR* 3.7 24.0 - - + -
4W ILE 2.9 16.1 + - - +
5W ASN* 3.8 14.1 - - - +
6W ALA 2.9 29.3 + - - +
62W THR 4.5 1.1 - - - +
63W ILE* 1.3 72.9 - - - +
65W VAL* 1.3 57.6 + - - +
66W ASP 4.2 0.8 + - - -
67W GLY* 3.8 32.1 - - - +
68W LYS 3.4 3.8 - - - +
69W GLU* 4.2 21.1 - - + +
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Residues in contact with VAL 65 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6W ALA 3.2 23.1 - - - +
7W GLU 4.0 1.1 - - - -
8W VAL* 3.8 26.7 - - + +
30W ILE* 4.8 0.2 - - + -
38W LEU* 4.2 8.3 - - + -
40W ILE* 4.0 14.6 - - + -
63W ILE* 3.9 25.8 - - + +
64W VAL* 1.3 75.1 - - - +
66W ASP* 1.3 75.6 + - - +
67W GLY 3.2 0.7 - - - -
68W LYS* 2.9 31.2 + - + +
70W ILE* 4.0 21.5 - - + -
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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