Contacts of the strand formed by residues 70 - 75 (chain B) in PDB entry 2HQR
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B ASP* 3.3 22.6 + - - +
47B LEU* 3.4 24.0 - - + -
48B VAL* 2.8 30.7 + - - +
69B ILE* 1.3 81.6 - - - +
71B VAL* 1.3 65.6 + - - +
92B ASP* 3.8 29.2 - - + +
93B ASP* 4.7 2.2 - - - +
112B ARG* 4.2 14.6 - - + +
113B LEU* 4.2 15.9 - - + -
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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
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48B VAL* 3.3 15.9 - - + +
50B VAL* 5.3 1.1 - - + -
59B VAL* 3.4 34.8 - - + -
62B ILE* 4.3 12.3 - - + -
63B LYS* 3.3 31.4 - - + +
69B ILE* 4.2 8.5 - - + -
70B VAL* 1.3 84.6 - - - +
72B LEU* 1.3 59.9 + - - +
73B VAL 4.0 1.3 + - - +
90B GLY 4.4 2.7 - - - +
91B ALA* 4.0 3.5 - - + -
92B ASP* 3.0 30.3 + - - +
93B ASP* 2.6 22.9 + - - +
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Residues in contact with LEU 72 (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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47B LEU* 3.8 19.9 - - + +
48B VAL 2.8 10.5 + - - -
49B MET* 3.2 33.6 - - + +
50B VAL 3.3 3.7 + - - -
71B VAL* 1.3 72.5 - - - +
73B VAL* 1.3 72.7 + - - +
74B SER* 3.8 10.1 - - - +
93B ASP* 3.1 30.5 - - - +
95B ILE* 3.7 18.8 - - + -
105B LEU* 3.8 14.6 - - + +
108B ARG* 5.6 1.3 - - + -
109B ILE* 3.7 32.3 - - + +
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Residues in contact with VAL 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B VAL* 3.5 9.4 - - - +
52B ASP 4.8 0.2 - - - +
55B ALA* 3.4 32.5 - - + -
56B LEU* 5.3 6.5 - - + -
59B VAL* 4.7 11.9 - - + -
71B VAL 4.0 1.6 + - - -
72B LEU* 1.3 78.8 - - - +
74B SER* 1.3 74.0 + - - +
75B SER* 5.7 0.7 - - - -
86B ALA* 4.4 7.2 - - + -
91B ALA* 4.0 17.0 - - + -
93B ASP 3.2 12.0 + - - +
94B TYR* 3.3 18.9 - - + -
95B ILE 3.1 21.7 + - - -
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Residues in contact with SER 74 (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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49B MET* 3.6 23.1 - - - +
50B VAL 3.2 5.6 + - - -
51B SER* 4.1 32.2 - - - +
52B ASP 4.9 2.3 - - - +
53B LYS* 6.0 0.5 - - - -
72B LEU* 3.8 4.7 - - - +
73B VAL* 1.3 87.4 + - - +
75B SER* 1.3 67.5 + - - +
94B TYR* 3.7 2.5 - - - -
95B ILE* 3.2 19.4 + - - +
97B LYS* 4.2 12.5 - - - -
99B TYR* 4.6 4.5 - - - -
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Residues in contact with SER 75 (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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51B SER 5.5 2.2 - - - -
53B LYS* 6.1 0.7 - - - +
73B VAL* 5.7 1.1 - - - -
74B SER* 1.3 81.2 - - - +
76B ASP* 1.3 61.1 + - - +
77B ASN* 2.8 13.1 + - - +
78B PRO* 3.4 3.6 - - - +
82B GLU* 2.5 37.0 + - - -
94B TYR* 2.9 27.0 + - - -
95B ILE 3.3 5.7 + - - -
97B LYS* 3.0 16.8 + - - +
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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