Contacts of the strand formed by residues 180 - 183 (chain S) in PDB entry 5JBA
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 MET 180 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98S THR 3.4 25.6 - - - +
99S TYR 3.7 7.0 - - - +
100S ASN* 3.6 24.5 - - - +
101S HIS 5.9 0.4 - - - +
165S ARG* 2.9 23.7 + - - -
175S THR 3.9 10.8 - - - +
176S ILE* 3.8 11.7 - - + -
177S THR* 3.1 38.3 + - + +
178S ASN 3.2 0.2 - - - -
179S ASN* 1.3 85.1 - - + +
181S PHE* 1.3 65.2 + - - +
214S SER* 6.4 0.4 - - - -
215S TRP* 3.5 21.8 - - + +
227S ILE* 3.9 9.6 - - + -
228S TYR 3.1 13.0 - - - +
229S THR* 5.2 1.1 - - - -
230S LYS* 3.5 10.5 - - - +
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Residues in contact with PHE 181 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131S LEU* 3.5 35.2 - - + -
162S LEU* 3.7 18.6 - - + -
163S VAL 5.8 0.2 - - - +
165S ARG* 4.6 4.7 - - - +
168S CYS* 4.4 3.4 - - - -
180S MET* 1.3 75.1 - - - +
182S CYS* 1.3 73.9 + - - +
183S ALA* 4.3 3.8 - - + -
199S HIS* 3.7 34.8 - + - -
210S THR 3.5 19.5 - - - -
211S GLY* 4.0 1.8 - - - -
227S ILE* 3.5 5.8 - - - +
228S TYR* 2.8 65.0 + + + +
229S THR 3.8 8.3 - - - -
230S LYS* 3.9 16.6 - - + -
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Residues in contact with CYS 182 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162S LEU* 3.5 3.3 - - - +
163S VAL* 3.1 35.9 + - + +
168S CYS* 2.1 61.1 - - + -
171S SER* 4.6 1.3 - - - -
176S ILE* 5.0 0.2 - - - -
181S PHE* 1.3 82.1 - - - +
183S ALA* 1.3 63.3 + - - +
225S TYR* 4.0 13.5 - - + -
226S GLY 3.3 3.8 - - - -
227S ILE* 3.5 23.1 - - - -
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Residues in contact with ALA 183 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160S VAL* 3.8 20.3 - - + +
161S PRO 3.2 17.3 - - - +
162S LEU* 4.4 2.0 - - - -
163S VAL* 4.1 4.9 - - - -
181S PHE* 4.3 10.3 - - + -
182S CYS* 1.3 75.6 - - - +
184S GLY* 1.3 58.2 + - - +
189S ASP* 4.8 1.2 - - - +
199S HIS* 4.6 2.5 - - - +
225S TYR* 3.8 2.3 - - - +
226S GLY* 3.0 32.6 + - - +
228S TYR* 3.8 21.9 + - + -
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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