Contacts of the strand formed by residues 180 - 184 (chain P) in PDB entry 1SXG
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 ILE 180 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169P VAL* 4.4 9.2 - - + -
172P LEU* 4.1 23.3 - - + -
173P ILE* 4.3 13.2 - - + -
177P HIS* 3.4 49.6 - - + +
178P LYS 3.5 9.1 + - - +
179P ASN* 1.3 71.0 - - - +
181P ALA* 1.3 64.5 + - - +
200P TYR* 2.6 40.2 + - + -
204P LEU* 4.2 22.8 - - + +
209P LEU* 4.4 0.2 - - + -
215P TYR* 3.4 8.2 - - - -
242P ALA* 3.3 15.0 - - + +
244P PHE* 4.7 3.6 - - + +
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Residues in contact with ALA 181 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180P ILE* 1.3 82.9 - - - +
182P PHE* 1.3 64.8 + - - +
200P TYR* 3.8 0.2 - - - -
215P TYR* 3.3 16.9 - - + +
233P LEU* 3.4 38.4 - - + -
240P PRO* 3.8 19.6 - - + +
242P ALA 2.9 6.7 + - - -
243P ILE* 4.2 4.3 - - + -
244P PHE* 3.0 21.5 + - - +
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Residues in contact with PHE 182 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181P ALA* 1.3 78.3 - - - +
183P VAL* 1.3 65.9 + - - +
184P SER* 3.1 34.1 - - - -
192P ASN* 5.0 1.1 - - - -
196P LYS* 4.2 15.3 - - + -
197P VAL* 4.2 31.4 - - + -
200P TYR* 3.7 29.2 - + + -
215P TYR 2.6 10.0 + - - +
216P ILE* 3.5 20.3 - - + -
217P VAL* 3.1 26.0 + - - +
243P ILE* 4.6 0.4 - - - -
244P PHE* 3.0 55.0 - + + +
246P GLY* 4.4 6.1 - - - -
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Residues in contact with VAL 183 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182P PHE* 1.3 72.2 - - - +
184P SER* 1.3 58.9 + - - +
217P VAL* 3.5 17.3 - - + +
219P GLY* 5.0 3.1 - - - +
226P GLY* 5.1 1.6 - - - -
229P ALA* 3.4 34.3 - - + -
233P LEU* 4.1 4.5 - - + -
243P ILE* 4.0 17.2 - - + +
244P PHE 2.9 8.4 + - - +
245P VAL* 3.3 18.9 - - + +
246P GLY 2.8 31.5 + - - -
250P MET* 4.1 25.1 - - + +
254P VAL* 4.0 9.4 - - + -
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Residues in contact with SER 184 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182P PHE* 3.1 31.4 + - - -
183P VAL* 1.3 75.2 - - - +
185P GLY* 1.3 75.3 + - - +
187P LEU* 3.9 12.4 - - - +
192P ASN* 3.3 22.0 + - - +
216P ILE* 5.1 2.2 - - - -
217P VAL 3.2 8.7 + - - -
218P GLU* 5.1 1.8 - - - -
219P GLY* 2.5 36.2 + - - -
246P GLY* 4.8 2.0 - - - +
250P MET* 3.8 6.1 - - - +
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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