Contacts of the strand formed by residues 134 - 138 (chain A) in PDB entry 2UVQ
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 134 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A PHE* 3.3 14.6 - - + +
26A ILE* 4.1 25.1 - - + -
58A LYS 3.2 2.4 + - - -
59A VAL* 3.4 22.9 - - + -
60A VAL 3.2 22.2 + - - -
132A ALA* 3.4 6.6 - - - +
133A ASP* 1.3 87.3 - - + +
135A VAL* 1.3 69.4 + - - +
136A LEU* 4.2 1.6 - - + +
227A ILE* 3.9 29.8 - - + -
230A ILE* 4.2 26.0 - - + -
231A LEU* 4.7 2.9 - - + -
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Residues in contact with VAL 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A PRO* 4.8 7.9 - - + -
24A PHE 2.9 9.9 + - - -
25A LEU* 3.3 22.4 - - + +
26A ILE 2.9 30.5 + - - +
60A VAL* 3.5 24.5 - - + +
62A LEU* 4.4 20.0 - - + -
101A LEU* 6.1 0.7 - - + -
104A ILE* 3.9 27.8 - - + -
129A VAL* 6.2 0.7 - - + -
132A ALA* 4.1 8.7 - - + +
134A VAL* 1.3 79.7 - - - +
136A LEU* 1.3 71.1 + - - +
137A PHE* 3.6 5.2 + - + +
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Residues in contact with LEU 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ILE* 3.4 38.4 - - + +
28A VAL* 4.7 7.0 - - + -
40A CYS* 4.1 31.4 - - + +
43A ILE* 4.0 32.8 - - + -
44A MET* 4.5 1.8 - - + -
59A VAL* 4.2 19.5 - - + -
60A VAL 3.0 9.1 + - - +
61A ILE* 3.2 19.0 - - + +
62A LEU* 2.7 32.1 + - - +
134A VAL* 4.2 1.3 - - + -
135A VAL* 1.3 73.0 - - - +
137A PHE* 1.3 53.7 + - - +
138A GLU 3.9 0.4 - - - -
156A LEU* 6.0 0.7 - - + -
223A ILE* 5.4 0.4 - - + -
227A ILE* 4.2 8.1 - - + -
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Residues in contact with PHE 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A LEU* 5.7 1.3 - - + -
26A ILE 2.9 10.5 + - - +
27A GLY* 3.5 1.7 - - - -
28A VAL* 2.9 25.5 + - - +
62A LEU* 3.1 45.5 - - + -
64A GLN* 4.0 15.3 - - - -
67A PHE* 4.3 2.9 - + - -
97A MET* 3.9 32.8 - - + -
101A LEU* 3.4 29.8 - - + -
135A VAL* 3.6 8.7 + - + +
136A LEU* 1.3 69.3 - - - +
138A GLU* 1.3 60.5 + - - +
142A VAL* 3.2 36.3 - - + +
148A ILE* 4.6 3.1 - - + -
152A PHE* 3.5 30.5 - + + -
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Residues in contact with GLU 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A VAL* 3.2 10.3 - - + +
36A LYS* 3.4 28.3 + - + +
37A SER* 3.1 24.4 + - - -
40A CYS* 4.0 21.1 - - - -
61A ILE* 4.1 13.0 - - + -
62A LEU 3.0 9.8 + - - +
63A SER* 2.6 31.0 + - - +
64A GLN* 3.0 24.7 + - - -
65A ASP* 4.5 7.9 + - - +
136A LEU 3.9 0.8 + - - -
137A PHE* 1.3 73.1 - - - +
139A GLY* 1.3 59.5 + - - +
142A VAL* 4.6 1.3 - - - -
1236A ADP 3.4 7.4 + - - -
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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