Contacts of the strand formed by residues 2 - 8 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MET* 1.3 77.4 - - - +
3A TYR* 1.3 59.9 + - - +
4A ILE* 3.8 1.8 - - + -
141A GLN 3.0 19.2 + - - +
142A VAL* 3.8 15.9 - - + +
143A CYS 2.8 27.0 + - - +
173A GLU* 2.7 33.4 + - - +
174A ASN* 2.7 28.5 + - - +
270A LEU* 2.8 46.8 + - + -
271A ASP 4.8 1.4 + - - -
272A LEU* 3.6 25.8 - - + -
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Residues in contact with TYR 3 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.2 56.2 - - + +
2A LYS* 1.3 71.7 - - - +
4A ILE* 1.3 61.5 + - - +
5A LEU* 3.4 2.5 + - - -
125A VAL* 3.4 28.9 - - + -
126A MET* 3.1 28.4 - - - +
129A ALA* 3.8 8.1 - - + +
143A CYS* 3.7 9.0 - - + -
145A ILE* 4.4 15.7 - - + -
166A PHE* 3.7 24.9 - + + -
170A VAL* 3.9 14.8 - - + -
174A ASN 2.7 20.5 + - - +
175A PHE* 3.3 19.9 - - + -
176A CYS 2.8 23.1 + - - +
270A LEU* 5.8 0.2 - - - +
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Residues in contact with ILE 4 (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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2A LYS* 4.9 0.4 - - + -
3A TYR* 1.3 71.7 - - - +
5A LEU* 1.3 59.6 + - - +
6A VAL* 3.7 2.1 + - + -
23A VAL* 4.9 6.5 - - + -
27A LEU* 3.8 20.6 - - + -
142A VAL* 3.6 27.8 - - + -
143A CYS 3.0 9.5 + - - +
144A VAL* 3.4 17.8 - - + +
145A ILE* 2.8 27.4 + - - -
176A CYS* 3.6 20.0 - - + -
178A ILE* 3.5 30.5 - - + -
266A PHE* 4.7 11.7 - - + -
270A LEU* 4.2 19.3 - - + -
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Residues in contact with LEU 5 (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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3A TYR 3.4 0.8 + - - -
4A ILE* 1.3 73.0 - - - +
6A VAL* 1.3 62.3 + - - +
7A THR* 3.6 23.1 - - + -
145A ILE* 3.8 22.9 - - + +
147A LEU* 3.9 13.0 - - + -
163A PHE* 3.6 56.3 - - + -
175A PHE* 3.8 27.1 - - + -
176A CYS 2.8 8.9 + - - +
177A ASN* 4.0 4.5 - - - +
178A ILE* 2.8 29.5 + - - +
209A LEU* 4.9 9.0 - - + -
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Residues in contact with VAL 6 (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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4A ILE* 4.4 4.3 - - + +
5A LEU* 1.3 73.7 - - - +
7A THR* 1.3 66.1 + - - +
16A LYS* 3.9 36.7 - - + +
19A ILE* 5.7 2.9 - - + -
20A ALA* 4.5 11.2 - - + +
144A VAL* 3.6 30.7 - - + -
145A ILE 2.7 15.3 + - - +
146A GLU* 4.3 5.6 - - + -
147A LEU* 3.0 28.9 + - - +
178A ILE* 3.7 16.8 - - + -
180A VAL* 4.2 9.6 - - + -
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Residues in contact with THR 7 (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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5A LEU* 3.6 30.3 - - + +
6A VAL* 1.3 79.2 - - - +
8A GLY* 1.3 59.9 + - - +
16A LYS* 3.6 7.3 - - - +
147A LEU* 4.3 17.9 - - + -
151A VAL* 5.1 6.5 - - - -
160A ILE* 5.4 3.4 - - + -
177A ASN* 3.8 9.7 + - - +
178A ILE 2.8 17.8 + - - +
179A HIS* 3.0 21.4 + - - +
180A VAL* 2.8 26.9 + - - +
204A LEU* 4.1 6.3 - - + +
209A LEU* 5.2 7.2 - - + -
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Residues in contact with GLY 8 (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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7A THR* 1.3 79.2 + - - +
9A GLY* 1.4 59.1 + - - -
14A ILE* 5.2 2.0 - - - -
16A LYS* 3.7 16.2 - - - +
149A GLY 4.0 3.7 - - - +
150A THR* 3.4 9.4 - - - -
151A VAL* 3.1 20.1 + - - +
179A HIS* 3.6 9.6 + - - -
180A VAL* 3.0 16.8 - - - -
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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