Contacts of the strand formed by residues 2 - 8 (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 LYS 2 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B MET* 1.3 76.7 - - - +
3B TYR* 1.3 58.8 + - - +
4B ILE* 3.8 1.1 - - + -
32B LEU* 6.2 0.2 - - + -
141B GLN 3.0 20.0 + - - +
142B VAL* 3.8 17.0 - - + +
143B CYS 2.8 27.2 + - - +
173B GLU* 2.7 33.1 + - - +
174B ASN* 2.7 28.5 + - - +
270B LEU* 2.8 45.3 + - + -
271B ASP* 4.8 1.6 + - - +
272B LEU* 3.6 26.5 - - + -
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Residues in contact with TYR 3 (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* 3.2 53.5 - - + +
2B LYS* 1.3 71.7 - - - +
4B ILE* 1.3 62.3 + - - +
5B LEU* 3.4 3.1 + - - -
125B VAL* 3.4 28.7 - - + -
126B MET* 3.1 28.1 - - - +
129B ALA* 3.8 9.2 - - + +
143B CYS* 3.7 9.4 - - + -
145B ILE* 4.4 15.5 - - + -
166B PHE* 3.7 25.4 - + + -
170B VAL* 3.9 15.0 - - + -
174B ASN 2.7 20.3 + - - +
175B PHE* 3.3 20.4 - - + +
176B CYS 2.8 23.3 + - - +
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Residues in contact with ILE 4 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B LYS* 4.9 0.2 - - + -
3B TYR* 1.3 72.4 - - - +
5B LEU* 1.3 60.2 + - - +
6B VAL* 3.7 1.7 + - + -
23B VAL* 4.9 6.5 - - + -
27B LEU* 3.8 20.4 - - + -
142B VAL* 3.6 27.8 - - + -
143B CYS 3.0 9.9 + - - +
144B VAL* 3.4 17.6 - - + +
145B ILE* 2.8 27.2 + - - +
176B CYS* 3.6 19.3 - - + -
178B ILE* 3.5 31.6 - - + -
266B PHE* 4.7 12.3 - - + -
270B LEU* 4.2 18.8 - - + -
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Residues in contact with LEU 5 (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 3.4 1.8 + - - +
4B ILE* 1.3 71.7 - - - +
6B VAL* 1.3 62.9 + - - +
7B THR* 3.6 23.6 - - + -
145B ILE* 3.8 22.2 - - + +
147B LEU* 3.9 12.3 - - + -
163B PHE* 3.6 57.2 - - + -
175B PHE* 3.8 26.2 - - + -
176B CYS 2.8 9.1 + - - +
177B ASN* 4.0 4.2 - - - +
178B ILE* 2.8 30.7 + - - +
209B LEU* 4.9 8.3 - - + -
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Residues in contact with VAL 6 (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* 4.4 4.0 - - + +
5B LEU* 1.3 75.0 - - - +
7B THR* 1.3 66.2 + - - +
16B LYS* 3.9 37.5 - - + +
19B ILE* 5.7 3.4 - - + -
20B ALA* 4.5 10.1 - - + +
144B VAL* 3.6 30.7 - - + -
145B ILE 2.7 16.1 + - - +
146B GLU* 4.3 5.4 - - - -
147B LEU* 3.0 29.3 + - - +
178B ILE* 3.7 16.2 - - + -
180B VAL* 4.2 9.6 - - + -
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Residues in contact with THR 7 (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* 3.6 30.3 - - + +
6B VAL* 1.3 78.9 - - - +
8B GLY* 1.3 59.2 + - - +
16B LYS* 3.7 6.9 - - - +
147B LEU* 4.3 17.3 - - + -
151B VAL* 5.1 7.0 - - - -
160B ILE* 5.4 2.9 - - + -
177B ASN* 3.8 10.9 + - - +
178B ILE 2.8 17.9 + - - +
179B HIS* 3.0 22.2 + - - +
180B VAL* 2.8 27.3 + - - +
204B LEU* 4.1 5.4 - - + +
209B LEU* 5.2 7.2 - - + -
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Residues in contact with GLY 8 (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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7B THR* 1.3 79.8 - - - +
9B GLY* 1.4 58.7 + - - -
14B ILE* 5.2 2.2 - - - -
16B LYS* 3.7 16.2 - - - +
149B GLY 4.0 2.5 - - - +
150B THR* 3.4 9.8 - - - -
151B VAL* 3.1 20.3 + - - +
179B HIS* 3.6 10.3 - - - -
180B VAL* 3.0 16.6 - - - -
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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