Contacts of the strand formed by residues 142 - 147 (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 VAL 142 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C MET* 3.5 4.9 - - - -
2C LYS* 3.6 20.6 - - + +
4C ILE* 3.6 32.3 - - + -
27C LEU* 3.9 14.1 - - + -
32C LEU* 4.0 18.8 - - + -
33C HIS 3.3 1.5 + - - +
34C VAL* 3.6 31.6 - - + -
35C THR* 2.9 28.1 + - - +
140C PRO 3.4 0.2 - - - -
141C GLN* 1.4 81.5 - - - +
143C CYS* 1.3 64.9 + - - +
144C VAL* 4.1 1.1 - - + -
270C LEU* 5.4 1.3 - - + -
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Residues in contact with CYS 143 (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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1C MET* 3.4 16.1 - - + -
2C LYS 2.8 10.2 + - - +
3C TYR* 3.7 10.7 - - + -
4C ILE* 3.0 24.4 + - - +
35C THR* 3.4 22.7 - - + -
36C SER* 3.8 5.8 - - - -
37C ILE* 3.6 38.6 - - - -
129C ALA* 5.5 3.1 - - - -
142C VAL* 1.3 74.1 - - - +
144C VAL* 1.3 64.1 + - - +
145C ILE* 3.8 13.2 + - - +
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Residues in contact with VAL 144 (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* 3.4 19.1 - - + +
6C VAL* 3.6 26.5 - - + -
20C ALA* 4.0 23.8 - - + +
23C VAL* 5.1 4.9 - - + -
24C GLY* 4.9 7.6 - - - -
27C LEU* 4.1 24.9 - - + -
34C VAL* 4.6 7.2 - - + -
35C THR 3.0 13.0 + - - +
36C SER* 3.0 13.4 - - - -
37C ILE 3.0 20.8 + - - +
142C VAL* 4.5 2.2 - - + -
143C CYS* 1.3 73.8 - - - +
145C ILE* 1.3 65.7 + - - +
146C GLU 3.9 0.5 + - - -
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Residues in contact with ILE 145 (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* 4.4 27.4 - - + -
4C ILE 2.8 14.1 + - - +
5C LEU* 3.8 19.9 - - + +
6C VAL* 2.7 33.7 + - - +
37C ILE* 3.2 22.4 - - + +
39C ILE* 3.6 29.4 - - + -
125C VAL* 4.7 10.1 - - + -
143C CYS* 3.9 18.8 - - - +
144C VAL* 1.3 76.2 - - - +
146C GLU* 1.3 60.3 + - - +
147C LEU 3.3 3.1 + - - -
163C PHE* 3.9 22.9 - - + -
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Residues in contact with GLU 146 (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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6C VAL* 4.2 7.4 - - + -
16C LYS* 4.4 15.8 - - + +
17C GLY* 3.6 8.0 + - - +
20C ALA* 5.1 2.7 - - + -
37C ILE 2.7 11.4 + - - +
38C LYS* 3.5 29.1 - - + +
39C ILE 2.8 28.5 + - - +
70C ASP* 3.3 13.2 - - - +
74C TYR* 2.4 38.6 + - + +
144C VAL* 3.9 2.6 + - - +
145C ILE* 1.3 70.8 - - - +
147C LEU* 1.3 63.0 + - - +
148C GLY* 3.5 1.1 + - - -
601C ATP 3.2 22.9 + - - -
602C UTP 3.6 13.0 - - - +
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Residues in contact with LEU 147 (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* 3.9 11.9 - - + -
6C VAL 3.0 21.8 + - - +
7C THR* 4.3 20.0 - - + -
16C LYS* 2.8 21.3 + - - -
39C ILE* 3.7 34.1 - - + +
41C PRO* 5.6 1.1 - - + -
145C ILE* 3.3 2.1 + - + -
146C GLU* 1.3 73.4 - - - +
148C GLY* 1.3 71.7 + - - +
156C SER* 4.9 8.1 - - - -
159C PHE* 4.0 24.7 - - + -
160C ILE* 4.4 20.0 - - + -
163C PHE* 4.3 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