Contacts of the strand formed by residues 70 - 76 (chain a) in PDB entry 5MQF
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 70 (chain a).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52a LEU* 5.9 5.4 - - + -
53a LEU 3.2 10.5 - - - +
54a GLY* 4.1 2.0 - - - -
67a LEU* 4.9 17.0 - - + +
68a GLU 3.4 0.4 - - - -
69a ASN* 1.3 72.6 - - - +
71a LYS* 1.3 60.3 + - - +
72a GLU* 3.8 4.9 + - + +
95a TYR* 3.6 7.4 - - - +
96a ILE* 2.6 53.6 + - + +
99a MET* 5.5 5.6 - - + -
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Residues in contact with LYS 71 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51a LYS 3.7 2.3 - - - +
52a LEU* 3.7 0.4 - - - -
53a LEU* 2.3 64.5 + - + +
69a ASN 3.4 3.3 + - - +
70a VAL* 1.3 66.0 - - - -
72a GLU* 1.3 58.9 + - - +
73a MET* 4.0 2.3 + - - +
94a ARG 4.2 3.1 - - - -
95a TYR* 5.3 0.9 - - - +
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Residues in contact with GLU 72 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50a LYS* 5.8 5.6 - - + -
51a LYS 3.2 10.3 - - - +
52a LEU* 4.7 4.5 - - + +
70a VAL* 3.8 5.8 - - + +
71a LYS* 1.3 72.3 - - - +
73a MET* 1.3 60.8 + - - +
93a ASP* 3.2 7.3 - - - +
94a ARG* 3.1 40.1 + - + +
96a ILE* 6.2 3.4 - - + -
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Residues in contact with MET 73 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50a LYS* 3.5 2.0 - - - +
51a LYS* 2.8 42.0 + - + +
71a LYS 4.0 2.6 + - - +
72a GLU* 1.3 73.7 - - - +
74a TRP* 1.3 61.9 + - - +
92a LYS 3.5 9.2 - - - +
93a ASP* 4.4 6.7 - - + -
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Residues in contact with TRP 74 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49a ASN 3.8 19.3 - - - +
50a LYS* 3.8 14.8 - - + -
73a MET* 1.3 78.3 - - - +
75a THR* 1.3 65.6 + - - +
91a ASN* 3.3 9.5 - - - +
92a LYS* 3.0 29.7 + - + +
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Residues in contact with THR 75 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49a ASN 4.9 1.8 + - - -
74a TRP* 1.3 80.8 - - - +
76a GLU* 1.3 64.5 + - - +
89a PRO* 5.3 7.9 - - - -
90a VAL 3.3 16.2 - - - -
91a ASN* 4.5 3.4 - - - -
92a LYS* 4.6 1.3 - - - +
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Residues in contact with GLU 76 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75a THR* 1.3 75.0 - - - +
77a VAL* 1.3 66.5 + - - +
88a LYS 3.8 1.6 - - - +
89a PRO* 3.8 3.8 - - - +
90a VAL* 2.8 36.9 + - + +
92a LYS* 5.8 5.8 - - + -
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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