Contacts of the strand formed by residues 59 - 66 (chain B) in PDB entry 3OVS
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 GLU 59 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B SER* 5.4 2.9 - - - -
48B TYR* 3.6 20.3 + - - +
53B TRP* 5.2 2.5 - - - +
57B SER 3.2 10.7 + - - +
58B LEU* 1.3 74.6 - - - +
60B ILE* 1.3 66.2 + - - +
61B ASP* 3.1 32.6 + - - +
101B HIS* 4.2 8.0 - - + -
108B GLU* 3.5 28.0 - - + +
109B VAL 4.5 0.2 - - - +
110B ASP* 3.5 25.6 - - - +
502B CTP 4.4 7.5 + - - +
34D C 4.1 6.9 + - - +
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Residues in contact with ILE 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLY* 4.1 17.9 - - - +
27B ALA* 4.4 9.4 - - + +
28B GLU* 4.5 7.6 - - + +
31B LEU* 4.6 4.7 - - + -
44B PHE* 3.7 29.8 - - + -
48B TYR* 4.1 30.7 - - + -
58B LEU* 5.1 2.0 - - + -
59B GLU* 1.3 76.7 - - - +
61B ASP* 1.3 61.8 + - - +
62B VAL* 4.3 5.8 - - + -
107B VAL* 3.7 24.0 - - + -
108B GLU 2.9 14.7 + - - +
109B VAL* 3.5 15.0 - - + +
110B ASP* 2.8 33.6 + - - +
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Residues in contact with ASP 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B PHE* 3.7 11.1 - - - -
45B VAL* 3.2 46.0 + - + +
46B GLY* 3.6 9.1 - - - +
47B SER 3.9 2.3 + - - -
48B TYR* 5.1 2.5 + - - +
59B GLU* 3.1 22.9 + - - +
60B ILE* 1.3 74.6 - - - +
62B VAL* 1.3 60.8 + - - +
63B PHE* 4.3 3.1 - - + -
110B ASP* 3.8 9.3 - - + +
112B VAL* 6.3 0.4 - - + -
502B CTP 3.1 30.1 + - - -
34D C 2.7 28.3 + - - +
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Residues in contact with VAL 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 3.5 30.5 - - + -
35B LEU* 4.0 24.7 - - + -
42B TYR* 4.4 12.1 - - + -
43B VAL 3.9 6.7 - - - +
44B PHE* 3.7 19.3 - - + -
60B ILE* 4.3 2.0 - - + -
61B ASP* 1.3 78.2 - - - +
63B PHE* 1.3 69.0 + - - +
64B LEU* 4.2 7.1 + - + -
109B VAL* 4.2 6.3 - - + -
110B ASP 2.9 16.7 + - - +
111B VAL* 3.5 8.1 - - + +
112B VAL* 2.9 26.4 + - - +
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Residues in contact with PHE 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B TYR* 3.3 4.9 - - - +
43B VAL* 2.7 58.6 + - + +
45B VAL* 3.3 26.7 - - + -
61B ASP* 5.1 3.1 - - + -
62B VAL* 1.3 81.9 - - - +
64B LEU* 1.3 63.1 + - - +
112B VAL* 3.3 27.8 - - + -
114B CYS* 3.5 22.9 - - - -
127B VAL* 3.6 37.7 - - + -
130B THR* 3.9 18.2 - - + -
131B PRO* 4.2 8.3 - - + -
34D C 3.9 25.4 - - - -
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Residues in contact with LEU 64 (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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35B LEU* 4.1 24.5 - - + -
40B VAL* 4.3 9.2 - - + -
41B GLU 3.8 6.1 - - - +
42B TYR* 4.6 4.3 - - + -
62B VAL* 4.7 3.4 - - + -
63B PHE* 1.3 74.9 - - - +
65B LEU* 1.3 60.8 + - - +
66B PHE* 3.7 17.8 + - + -
79B GLY* 3.8 35.2 - - - +
82B ILE* 3.8 19.5 - - + -
111B VAL* 3.8 27.1 - - + -
112B VAL 3.0 8.7 + - - +
113B PRO* 3.8 7.4 - - + +
114B CYS* 2.8 35.6 + - - +
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Residues in contact with LEU 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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40B VAL* 6.1 0.3 - - - +
41B GLU* 3.3 41.4 + - + +
42B TYR 4.6 4.7 - - - +
43B VAL* 3.8 41.3 - - + +
63B PHE 4.6 0.2 - - - +
64B LEU* 1.3 70.6 - - - +
66B PHE* 1.3 63.8 + - - +
67B PRO* 4.0 5.5 - - - +
114B CYS* 3.8 12.8 - - - -
115B TYR 3.7 22.2 - - - +
116B LYS* 3.9 23.6 - - + -
131B PRO* 4.5 9.0 - - + -
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Residues in contact with PHE 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B VAL* 5.9 1.3 - - + -
64B LEU* 3.7 19.5 - - + -
65B LEU* 1.3 74.6 - - - +
67B PRO* 1.3 79.2 - - + +
68B GLU 3.6 1.4 + - - -
70B PHE* 5.2 15.0 - + + -
75B LEU* 3.6 33.7 - - + -
78B ARG* 3.7 23.6 - - + -
79B GLY* 3.6 24.2 - - - -
82B ILE* 4.0 16.6 - - + -
113B PRO* 3.6 22.9 - - + -
114B CYS 3.0 15.4 + - - +
115B TYR* 3.6 8.9 - - + -
116B LYS* 3.4 21.0 + - - -
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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
------------------------------------------------------------
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