Contacts of the strand formed by residues 161 - 165 (chain G) in PDB entry 3SZ9
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 161 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63G VAL* 4.3 7.9 - - + +
66G ALA* 4.0 16.6 - - + -
67G ARG* 3.4 47.3 - - + +
70G PHE* 5.0 0.7 - - + -
160G GLY* 1.3 69.2 - - - -
162G CYS* 1.3 60.8 + - - +
188G VAL* 3.7 17.7 - - + +
190G VAL* 4.4 9.6 - - + -
237G ASP 3.7 12.6 - - - +
238G VAL* 3.7 23.7 - - + +
239G ASP* 2.8 38.2 + - - +
240G LYS 3.3 5.5 + - - -
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Residues in contact with CYS 162 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159G VAL* 3.5 31.4 - - - -
160G GLY 3.6 4.5 - - - -
161G VAL* 1.3 73.0 - - - +
163G GLY* 1.3 62.3 - - - +
164G GLN* 3.7 11.1 + - + +
187G ASN* 3.6 17.0 - - - -
188G VAL 2.8 14.8 + - - +
189G VAL* 3.4 6.7 - - + -
190G VAL 2.9 24.8 + - - +
238G VAL* 4.5 0.2 - - - -
240G LYS* 3.3 12.8 - - + +
485G TYR* 3.7 28.7 - - + -
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Residues in contact with GLY 163 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162G CYS* 1.3 74.1 - - - +
164G GLN* 1.3 61.8 + - - +
165G ILE 4.2 0.2 - - - -
190G VAL* 3.3 11.4 - - - -
232G ILE* 3.6 25.1 - - - -
238G VAL* 3.7 8.1 - - - +
240G LYS 2.7 14.5 + - - +
241G VAL* 3.3 5.3 - - - -
242G ALA 2.8 26.5 + - - -
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Residues in contact with GLN 164 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162G CYS* 4.1 10.3 - - + +
163G GLY* 1.3 79.9 - - - +
165G ILE* 1.3 61.5 + - - +
166G ILE* 4.8 0.7 - - - -
178G LYS* 3.0 41.6 + - + +
179G LEU* 3.9 2.9 - - - +
182G ALA* 3.7 4.6 - - - +
189G VAL* 3.1 28.0 - - + +
190G VAL 2.9 10.0 + - - +
191G MET* 3.3 28.8 - - + +
192G LYS 2.8 26.3 + - - -
232G ILE* 4.7 1.0 - - - +
242G ALA* 3.5 4.7 - - + -
485G TYR* 2.9 36.2 + - - +
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Residues in contact with ILE 165 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164G GLN* 1.3 75.6 - - - +
166G ILE* 1.3 71.1 + - - +
178G LYS* 4.4 0.7 - - - -
192G LYS* 3.6 32.1 - - + +
229G GLY* 3.8 25.8 - - - +
232G ILE* 4.7 9.9 - - + -
233G ALA 5.1 0.4 - - - +
241G VAL* 4.3 14.4 - - + -
242G ALA 2.9 9.5 + - - +
243G PHE* 3.5 27.9 - - + -
244G THR 3.1 24.7 + - - +
253G ILE* 3.8 28.9 - - + -
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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