Contacts of the strand formed by residues 70 - 74 (chain B) in PDB entry 6D6Q
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 LEU 70 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B ILE* 5.3 5.8 - - + -
63B ARG* 4.4 40.2 - - + +
64B ALA* 5.7 1.6 - - - -
65B LEU* 4.5 17.5 - - + +
69B ALA* 1.3 72.5 - - - +
71B VAL* 1.3 75.8 + - - +
72B ASN* 3.7 10.3 + - + -
107B GLU* 5.7 2.2 - - - +
117B ARG* 6.3 0.2 - - - -
118B SER 2.8 20.2 + - - +
119B GLN* 3.3 23.3 - - + +
120B ILE 2.9 25.6 + - - +
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Residues in contact with VAL 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ALA 4.0 1.7 + - - +
70B LEU* 1.3 81.8 - - - +
72B ASN* 1.3 63.9 + - - +
73B CYS* 4.1 1.3 - - + +
103B ARG* 3.6 37.7 - - + +
106B PHE* 4.8 4.5 - - + -
107B GLU* 3.4 36.1 + - + +
110B ILE* 4.3 10.5 - - + -
112B THR* 4.2 21.3 - - + -
120B ILE* 3.6 13.9 - - + +
122B ILE* 4.2 25.1 - - + -
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Residues in contact with ASN 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ARG* 4.9 15.9 - - - +
70B LEU* 3.7 13.2 + - + +
71B VAL* 1.3 73.9 - - - +
73B CYS* 1.3 66.3 + - - +
74B GLN* 5.3 2.4 - - - +
103B ARG* 5.1 1.3 - - - +
119B GLN* 5.3 2.8 - - - +
120B ILE 3.0 8.5 + - - -
121B ASP* 3.4 24.2 + - - +
122B ILE 2.9 25.1 + - - +
123B TYR* 5.1 8.4 + - - -
94E GLU* 4.0 19.8 + - - -
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Residues in contact with CYS 73 (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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71B VAL* 4.1 1.5 + - + -
72B ASN* 1.3 79.8 + - - +
74B GLN* 1.3 61.2 + - - +
99B GLY* 2.9 40.3 - - - +
102B LEU* 3.6 15.7 - - + -
103B ARG* 3.2 32.9 - - - +
122B ILE* 3.1 32.3 - - + -
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Residues in contact with GLN 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ASN* 5.3 2.7 - - - +
73B CYS* 1.3 74.7 - - - +
75B TYR* 1.3 70.2 + - - +
76B SER* 5.8 2.0 - - - -
90B HIS* 4.6 13.5 - - - +
99B GLY* 5.3 0.7 - - - -
102B LEU* 4.9 3.0 - - - +
122B ILE 2.9 6.3 + - - -
123B TYR* 3.1 36.5 - - + -
124B VAL* 2.9 32.3 + - - +
87E ALA* 3.7 13.1 - - - +
94E GLU* 4.2 12.4 - - - +
95E GLY* 3.9 23.6 - - - +
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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