Contacts of the strand formed by residues 142 - 147 (chain B) in PDB entry 5U03
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 142 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET* 3.5 4.5 - - - -
2B LYS* 3.6 20.9 - - + +
4B ILE* 3.6 32.3 - - + -
27B LEU* 3.9 13.7 - - + -
32B LEU* 4.0 18.4 - - + -
33B HIS 3.6 1.5 - - - +
34B VAL* 3.6 32.5 - - + -
35B THR* 2.9 27.9 + - - +
140B PRO 3.4 0.6 - - - -
141B GLN* 1.4 80.9 - - - +
143B CYS* 1.3 65.7 + - - +
144B VAL* 4.1 1.1 - - + -
270B LEU* 5.4 1.6 - - + -
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Residues in contact with CYS 143 (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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1B MET* 3.4 15.9 - - + -
2B LYS 2.8 11.5 + - - +
3B TYR* 3.7 9.6 - - + -
4B ILE* 3.0 24.8 + - - +
35B THR* 3.4 23.3 - - + -
36B SER* 3.8 6.3 - - - -
37B ILE* 3.6 37.2 - - - -
129B ALA* 5.5 3.4 - - - -
142B VAL* 1.3 73.9 - - - +
144B VAL* 1.3 64.6 + - - +
145B ILE* 3.8 12.8 + - - +
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Residues in contact with VAL 144 (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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4B ILE* 3.4 18.4 - - + +
6B VAL* 3.6 27.4 - - + -
20B ALA* 4.0 23.6 - - + +
23B VAL* 5.1 4.5 - - + -
24B GLY* 4.9 8.1 - - - -
27B LEU* 4.1 24.9 - - + -
34B VAL* 4.6 7.6 - - + -
35B THR 3.0 12.2 + - - +
36B SER* 3.0 13.7 - - - -
37B ILE 3.0 20.8 + - - +
142B VAL* 4.5 1.6 - - + -
143B CYS* 1.3 76.4 - - - +
145B ILE* 1.3 61.2 + - - +
146B GLU 3.9 0.7 + - - +
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Residues in contact with ILE 145 (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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3B TYR* 4.4 27.6 - - + -
4B ILE 2.8 13.8 + - - +
5B LEU* 3.8 20.1 - - + +
6B VAL* 2.7 32.7 + - - +
37B ILE* 3.2 20.9 - - + +
39B ILE* 3.6 30.1 - - + -
125B VAL* 4.7 9.9 - - + -
143B CYS* 3.9 18.4 - - - +
144B VAL* 1.3 77.1 - - - +
146B GLU* 1.3 61.4 + - - +
147B LEU 3.3 2.9 + - - -
163B PHE* 3.9 22.7 - - + -
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Residues in contact with GLU 146 (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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6B VAL* 4.2 7.4 - - + -
16B LYS* 4.5 15.8 - - + -
17B GLY* 3.6 7.1 + - - +
20B ALA* 5.1 2.2 - - + -
37B ILE 2.7 11.7 + - - +
38B LYS* 3.5 29.1 - - + +
39B ILE 2.8 28.2 + - - +
70B ASP* 3.3 13.4 - - - +
74B TYR* 2.4 38.6 + - + +
144B VAL* 3.9 2.6 + - - +
145B ILE* 1.3 70.2 - - - +
147B LEU* 1.3 64.0 + - - +
148B GLY* 3.5 0.9 + - - -
601B ATP 3.2 23.4 + - - -
602B UTP 3.6 12.5 - - - +
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Residues in contact with LEU 147 (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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5B LEU* 3.9 11.9 - - + -
6B VAL 3.0 22.6 + - - +
7B THR* 4.3 20.2 - - + -
16B LYS* 2.8 21.5 + - - -
39B ILE* 3.7 33.9 - - + -
41B PRO* 5.6 1.3 - - + -
145B ILE* 3.3 2.1 + - + -
146B GLU* 1.3 73.4 - - - +
148B GLY* 1.3 70.9 + - - +
156B SER* 4.9 8.3 - - - -
159B PHE* 4.0 23.8 - - + -
160B ILE* 4.4 20.0 - - + -
163B PHE* 4.3 15.9 - - + -
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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