Contacts of the strand formed by residues 64 - 72 (chain B) in PDB entry 3V6R
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 TYR 64 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B TYR* 2.8 35.0 + - - -
60B VAL* 4.0 5.8 - - + +
61B LEU* 3.0 23.1 + - + +
63B ARG* 1.3 98.6 + - + +
65B GLN* 1.3 54.9 + - - +
67B LEU* 3.5 4.4 - - + +
81B ALA* 4.2 4.7 - - + -
82B TYR 3.4 2.7 - - - -
83B ASP* 3.3 30.3 + - + -
90B VAL* 3.8 19.1 - - + -
92B ILE* 3.6 23.6 - - + -
128B ASN* 2.9 34.7 + - - +
130B PHE* 3.6 25.1 - + - -
145B VAL* 3.7 22.0 - - + +
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Residues in contact with GLN 65 (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 TYR* 3.7 8.5 - - + +
62B LYS 3.4 20.8 + - - +
63B ARG* 4.3 0.6 - - - +
64B TYR* 1.3 76.9 - - - +
66B ASN* 1.4 77.5 + - - +
67B LEU* 3.3 4.5 + - - -
81B ALA* 3.5 2.8 - - - +
82B TYR* 2.8 49.3 + - - +
84B ALA* 3.5 28.8 - - - +
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Residues in contact with ASN 66 (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 TYR* 4.6 1.8 + - - -
65B GLN* 1.4 86.3 - - - +
67B LEU* 1.4 63.4 + - - +
68B LYS* 3.4 24.9 + - - +
80B ALA 3.8 3.8 - - - +
81B ALA* 4.2 2.6 - - - -
82B TYR* 4.0 20.7 + - + +
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Residues in contact with LEU 67 (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 TYR* 3.5 25.1 + - - +
51B VAL* 3.8 27.3 - - + +
53B VAL* 3.8 24.8 - - + +
58B PHE* 3.9 15.7 - - + -
60B VAL* 4.1 15.3 - - + -
64B TYR* 3.5 16.4 - - + +
65B GLN 3.3 1.6 - - - -
66B ASN* 1.4 72.8 - - - +
68B LYS* 1.4 60.2 + - - +
69B PRO* 4.6 1.2 - - - +
79B CYS* 3.6 25.8 - - - -
80B ALA 3.2 4.9 - - - -
81B ALA* 3.8 17.5 - - + -
92B ILE* 5.0 1.6 - - + -
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Residues in contact with LYS 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B VAL* 3.9 0.7 - - - -
66B ASN* 3.4 23.1 - - - +
67B LEU* 1.4 75.6 - - - +
69B PRO* 1.4 71.4 - - + +
70B ILE* 5.6 1.3 - - + -
79B CYS* 3.2 4.2 - - - +
80B ALA* 2.7 51.4 + - + +
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Residues in contact with PRO 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B VAL* 3.5 24.4 - - + -
54B GLY* 4.4 18.6 - - - +
67B LEU 4.6 1.1 - - - +
68B LYS* 1.4 88.9 - - + +
70B ILE* 1.3 64.5 + - - +
71B GLY 5.4 0.7 - - - +
72B SER* 6.4 1.8 - - - -
78B VAL 4.3 2.9 - - - +
79B CYS* 4.1 3.6 - - + -
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Residues in contact with ILE 70 (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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68B LYS* 4.2 1.8 - - + +
69B PRO* 1.3 77.8 - - - +
71B GLY* 1.3 62.4 + - - +
78B VAL* 3.4 18.1 + - + +
79B CYS* 3.6 22.2 - - - +
80B ALA* 3.9 17.7 - - + -
91B ALA* 4.3 0.9 - - + -
148B LEU* 3.8 22.0 - - + -
403B CQQ 3.0 67.5 - - + +
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Residues in contact with GLY 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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69B PRO* 6.4 0.7 - - - -
70B ILE* 1.3 80.2 - - - +
72B SER* 1.3 60.2 - - - -
73B GLY 4.2 1.1 - - - -
76B GLY 3.7 5.8 - - - +
77B ILE* 3.8 2.9 - - - +
78B VAL* 2.8 49.3 + - - +
403B CQQ 3.7 14.6 - - - -
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Residues in contact with SER 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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54B GLY* 4.7 11.7 + - - -
69B PRO* 6.4 1.8 - - - -
70B ILE 4.4 0.4 + - - -
71B GLY* 1.3 73.4 - - - -
73B GLY* 1.3 61.4 + - - +
76B GLY 4.6 3.4 - - - -
77B ILE* 5.2 12.1 - - - +
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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