Contacts of the strand formed by residues 61 - 65 (chain B) in PDB entry 2O07
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 ASN 61 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B LEU* 3.3 30.7 - - + +
53B VAL* 4.8 3.6 - - + -
54B PHE 3.4 3.6 - - - +
55B ARG* 3.5 19.2 + - - +
60B GLY* 1.3 73.4 - - - -
62B VAL* 1.3 60.3 + - - +
63B LEU 4.3 0.2 - - - -
71B CYS 4.0 0.5 - - - +
72B THR* 3.2 4.9 - - - -
73B GLU* 2.8 49.2 + - + +
136B PHE* 2.6 35.1 + - - +
137B LEU* 4.2 6.9 - - + +
138B PRO* 5.1 1.6 - - - +
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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
----------------------------------------------------------
35B LEU* 4.1 6.1 - - + -
52B LEU 3.7 0.7 - - - +
53B VAL* 3.2 10.8 - - - +
54B PHE* 2.8 70.5 + - + +
56B SER* 3.8 9.0 - - - +
60B GLY 3.7 10.8 - - - +
61B ASN* 1.3 80.4 - - - +
63B LEU* 1.3 63.3 + - - +
64B VAL* 3.8 15.5 - - + -
69B ILE* 4.2 16.6 - - + -
71B CYS 3.4 10.1 - - - +
72B THR* 3.9 17.9 - - + -
137B LEU* 5.3 1.1 - - - -
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Residues in contact with LEU 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ILE* 3.9 21.8 - - + -
52B LEU 3.7 1.1 - - - +
53B VAL* 3.8 22.9 - - + -
61B ASN 4.3 0.4 - - - -
62B VAL* 1.3 72.2 - - - +
64B VAL* 1.3 61.8 + - - +
65B LEU* 4.1 9.0 - - + -
69B ILE* 3.7 3.3 - - - -
70B GLN* 2.7 51.0 + - + -
71B CYS* 3.0 18.3 + - - +
104B ASP* 4.7 1.1 - - + -
129B VAL* 4.2 16.4 - - + -
132B VAL* 4.4 5.2 - - + -
133B SER* 4.2 10.3 - - - +
137B LEU* 4.0 31.5 - - + +
501B MTA 4.2 9.4 - - + -
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Residues in contact with VAL 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B PHE* 3.6 24.0 - - + -
50B ASP 3.6 0.7 - - - +
52B LEU* 2.8 51.9 + - + +
54B PHE* 3.9 17.0 - - + -
62B VAL* 3.8 20.0 - - + +
63B LEU* 1.3 79.7 - - - +
65B LEU* 1.3 66.8 + - - +
66B ASP 4.3 0.4 - - - -
67B GLY* 3.4 40.4 - - - +
68B VAL 3.4 7.0 - - - +
69B ILE* 4.5 3.4 - - + -
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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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49B GLN* 3.6 24.2 - - - +
50B ASP 3.2 5.6 - - - +
51B ILE* 3.6 34.5 - - + -
63B LEU* 4.1 7.9 - - + -
64B VAL* 1.3 79.9 - - - +
66B ASP* 1.3 73.6 + - - +
67B GLY 3.1 0.4 - - - -
68B VAL* 2.9 27.8 + - - +
70B GLN* 3.5 32.5 - - + +
129B VAL* 3.9 13.5 - - + -
175B SER* 5.2 5.4 + - - +
501B MTA 3.7 33.4 - - + +
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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