Contacts of the strand formed by residues 78 - 85 (chain B) in PDB entry 2V5Q
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 78 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69B GLU* 4.2 14.1 - - + +
70B ILE 3.3 11.0 - - - +
71B SER* 4.3 8.5 - - - -
76B LYS 3.7 14.4 - - - +
77B GLU* 1.3 73.6 - - - +
79B PHE* 1.3 73.9 + - - +
132B LEU* 3.5 34.2 + - + +
134B ARG* 4.2 16.8 - - - +
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Residues in contact with PHE 79 (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 ARG* 5.9 4.3 - - - -
53B TYR* 4.1 27.4 - + - -
69B GLU* 3.3 6.6 - - - -
70B ILE* 2.7 42.1 + - + -
72B ASP* 4.8 5.8 - - + -
77B GLU* 3.6 48.9 - - + -
78B VAL* 1.3 79.1 - - - +
80B ALA* 1.3 61.1 + - - +
117B HIS* 3.6 38.4 - + + -
129B VAL* 3.6 20.0 - - + -
130B LEU 3.4 15.5 - - - +
131B GLU* 4.9 2.0 - - - -
132B LEU* 4.0 10.9 - - - +
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Residues in contact with ALA 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B LEU* 4.5 8.3 - - + -
67B CYS* 5.8 3.1 - - + -
68B PHE 3.5 5.6 - - - +
70B ILE* 4.1 1.3 - - - -
79B PHE* 1.3 72.4 - - - +
81B GLY* 1.3 60.5 + - - +
82B LYS* 4.0 0.8 + - + -
128B VAL 3.4 2.1 - - - +
129B VAL* 3.6 2.6 - - - -
130B LEU* 2.8 51.5 + - + +
131B GLU 4.0 13.5 - - - +
132B LEU* 4.0 17.6 - - + +
133B CYS 5.4 0.2 - - - +
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Residues in contact with GLY 81 (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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44B LEU* 5.4 2.0 - - - -
66B LYS 3.6 1.6 - - - +
67B CYS* 3.2 4.9 - - - -
68B PHE* 2.6 43.4 + - - -
70B ILE* 3.7 25.3 - - - +
80B ALA* 1.3 72.1 - - - +
82B LYS* 1.3 60.9 - - - -
83B ILE* 4.0 9.6 - - - +
127B PHE* 6.5 0.4 - - - -
128B VAL 3.4 6.5 - - - -
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Residues in contact with LYS 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B GLY 4.7 9.6 + - - -
65B ALA* 3.6 24.7 - - + -
66B LYS 3.6 3.8 - - - -
67B CYS* 4.3 16.2 - - - -
80B ALA* 4.0 0.8 - - + -
81B GLY* 1.3 71.6 - - - -
83B ILE* 1.3 62.5 + - - +
84B VAL* 4.1 13.3 + - + +
98B MET* 5.1 6.1 - - - -
101B GLU* 3.8 27.5 + - - -
126B VAL 3.6 3.6 - - - +
127B PHE* 3.6 0.9 - - - -
128B VAL* 2.8 49.1 + - + +
130B LEU* 4.4 21.8 - - + -
194B ASP* 5.1 11.1 + - - +
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Residues in contact with ILE 83 (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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40B ILE* 3.6 36.1 - - + -
44B LEU* 4.2 20.2 - - + -
55B ARG* 5.2 1.8 - - + -
65B ALA* 3.3 2.6 - - - -
66B LYS* 2.8 37.9 + - - +
68B PHE* 3.7 24.5 - - + -
70B ILE* 5.6 0.7 - - + -
81B GLY* 4.1 9.6 - - - +
82B LYS* 1.3 77.7 - - - +
84B VAL* 1.3 62.6 + - - +
85B PRO* 3.8 4.5 - - - +
125B PHE* 3.5 26.8 - - + -
126B VAL 3.6 1.8 - - - -
127B PHE* 3.7 24.9 - - + -
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Residues in contact with VAL 84 (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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64B PHE* 4.1 17.9 - - + -
65B ALA* 3.7 19.7 - - + +
82B LYS* 4.4 15.7 - - + +
83B ILE* 1.3 74.1 - - - +
85B PRO* 1.3 80.2 - - + +
86B LYS* 3.4 0.5 + - - -
88B LEU* 5.4 0.2 - - + -
89B LEU* 3.8 26.0 - - + +
98B MET* 4.1 23.1 - - + -
125B PHE* 3.2 4.2 - - - -
126B VAL* 2.8 43.8 + - + +
128B VAL* 5.8 1.3 - - + -
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Residues in contact with PRO 85 (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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64B PHE 3.4 20.2 - - - +
66B LYS* 6.5 1.3 - - + -
83B ILE 3.8 5.4 - - - +
84B VAL* 1.3 86.6 - - + +
86B LYS* 1.3 62.0 + - - +
87B SER* 3.1 21.8 - - - +
88B LEU* 3.1 30.0 + - + +
89B LEU* 3.7 11.4 - - - +
124B ASP 3.4 8.7 - - - +
125B PHE* 3.6 18.4 - - + -
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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