Contacts of the strand formed by residues 2 - 8 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1C MET* 1.3 77.0 - - - +
3C TYR* 1.3 59.8 + - - +
4C ILE* 3.8 1.3 - - + -
32C LEU* 6.2 0.2 - - + -
141C GLN 3.0 20.6 + - - +
142C VAL* 3.8 16.4 - - + -
143C CYS 2.8 26.9 + - - +
173C GLU* 2.7 33.1 + - - +
174C ASN* 2.7 29.1 + - - +
270C LEU* 2.8 46.2 + - + -
271C ASP* 4.8 1.2 + - - +
272C LEU* 3.6 26.0 - - + -
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Residues in contact with TYR 3 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MET* 3.2 55.9 - - + +
2C LYS* 1.3 71.9 - - - +
4C ILE* 1.3 62.4 + - - +
5C LEU* 3.4 2.9 + - - -
125C VAL* 3.4 28.9 - - + -
126C MET* 3.1 28.2 - - - +
129C ALA* 3.8 8.5 - - + +
143C CYS* 3.7 9.4 - - + -
145C ILE* 4.4 15.0 - - + -
166C PHE* 3.7 26.2 - + + -
170C VAL* 3.9 14.5 - - + +
174C ASN 2.7 20.4 + - - +
175C PHE* 3.3 20.9 - - + +
176C CYS 2.8 23.5 + - - +
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Residues in contact with ILE 4 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C LYS* 4.9 0.4 - - + -
3C TYR* 1.3 71.5 - - - +
5C LEU* 1.3 61.3 + - - +
6C VAL* 3.7 2.1 + - + -
23C VAL* 4.9 7.0 - - + -
27C LEU* 3.8 19.5 - - + -
142C VAL* 3.6 28.5 - - + -
143C CYS 3.0 10.1 + - - +
144C VAL* 3.4 17.5 - - + +
145C ILE* 2.8 27.6 + - - -
176C CYS* 3.6 18.8 - - + -
178C ILE* 3.5 31.6 - - + -
266C PHE* 4.7 11.7 - - + -
270C LEU* 4.2 20.2 - - + -
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Residues in contact with LEU 5 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C TYR 3.4 1.0 + - - -
4C ILE* 1.3 72.5 - - - +
6C VAL* 1.3 61.6 + - - +
7C THR* 3.6 23.8 - - + -
145C ILE* 3.8 22.0 - - + +
147C LEU* 3.9 12.3 - - + -
163C PHE* 3.6 57.2 - - + -
175C PHE* 3.8 27.1 - - + -
176C CYS 2.8 8.9 + - - +
177C ASN* 3.9 4.1 - - - +
178C ILE* 2.8 30.2 + - - +
209C LEU* 4.9 9.0 - - + -
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Residues in contact with VAL 6 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C ILE* 4.4 3.8 - - + +
5C LEU* 1.3 74.4 - - - +
7C THR* 1.3 65.2 + - - +
16C LYS* 3.9 36.1 - - + +
19C ILE* 5.7 3.4 - - + -
20C ALA* 4.5 10.3 - - + +
144C VAL* 3.6 31.9 - - + -
145C ILE 2.7 15.8 + - - +
146C GLU* 4.3 5.8 - - + -
147C LEU* 3.0 29.6 + - - +
178C ILE* 3.7 16.4 - - + -
180C VAL* 4.2 9.6 - - + -
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Residues in contact with THR 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C LEU* 3.6 30.5 - - + +
6C VAL* 1.3 79.0 - - - +
8C GLY* 1.3 60.2 + - - +
16C LYS* 3.7 6.9 - - - +
147C LEU* 4.3 17.0 - - + -
151C VAL* 5.1 6.5 - - - -
160C ILE* 5.4 3.4 - - + -
177C ASN* 3.8 9.8 + - - +
178C ILE 2.8 17.8 + - - +
179C HIS* 3.0 22.2 + - - +
180C VAL* 2.8 26.6 + - - +
204C LEU* 4.1 5.5 - - + +
209C LEU* 5.2 7.4 - - + -
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Residues in contact with GLY 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C THR* 1.3 80.6 + - - +
9C GLY* 1.4 59.6 + - - -
11C ILE 6.0 0.2 - - - -
14C ILE* 5.2 2.0 - - - -
16C LYS* 3.7 15.5 - - - +
149C GLY 4.0 2.7 - - - +
150C THR* 3.4 10.2 - - - -
151C VAL* 3.1 20.3 + - - +
179C HIS* 3.6 9.2 - - - -
180C 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