Contacts of the strand formed by residues 188 - 192 (chain C) 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 188 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C ALA* 3.3 37.7 - - + +
69C ALA* 4.2 7.0 - - + -
70C PHE* 4.0 14.5 - - + +
76C TRP* 3.6 27.8 - - + -
160C GLY 3.1 12.1 + - - +
161C VAL* 3.8 11.0 - - + -
162C CYS* 2.7 35.1 + - - +
187C ASN* 1.3 71.6 - - - +
189C VAL* 1.3 61.0 + - - +
216C GLY 3.9 7.9 - - - +
217C VAL* 3.4 21.3 - - - +
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Residues in contact with VAL 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162C CYS* 3.3 3.8 - - + +
164C GLN* 3.1 33.9 - - - +
179C LEU* 3.9 21.3 - - + -
182C ALA* 3.9 24.2 - - + -
183C LEU* 4.5 7.6 - - + -
188C VAL* 1.3 84.5 - - - +
190C VAL* 1.3 76.0 + - - +
191C MET* 4.0 9.4 - - + +
217C VAL 2.9 13.1 + - - +
218C VAL* 4.4 6.3 - - + -
219C ASN* 2.9 33.5 + - - -
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Residues in contact with VAL 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C VAL* 4.9 2.0 - - + +
62C ALA* 3.7 47.3 - - + +
63C VAL* 4.0 14.6 - - + -
66C ALA* 3.8 11.9 - - + -
161C VAL* 4.2 9.9 - - + -
162C CYS 2.9 9.6 + - - +
163C GLY* 3.2 8.1 - - - -
164C GLN 2.9 23.6 + - - +
189C VAL* 1.3 79.1 - - - +
191C MET* 1.3 61.0 + - - +
219C ASN* 3.5 5.2 - - - +
221C VAL* 4.5 9.2 - - + -
232C ILE* 4.2 26.0 - - + +
238C VAL* 5.7 0.7 - - + -
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Residues in contact with MET 191 (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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164C GLN* 3.1 35.9 - - + +
166C ILE* 4.0 15.3 - - + -
175C GLN* 3.9 39.0 - - - +
178C LYS* 3.8 18.4 - - + -
179C LEU* 3.9 16.6 - - + -
189C VAL* 4.0 7.9 - - + -
190C VAL* 1.3 75.1 - - - +
192C LYS* 1.3 62.0 + - - +
193C VAL* 4.2 13.5 - - + -
218C VAL* 5.4 0.2 - - + -
219C ASN 2.9 13.0 + - - +
220C ILE* 3.4 15.1 - - + +
221C VAL* 2.9 28.1 + - - +
232C ILE* 4.6 2.9 - - - -
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Residues in contact with LYS 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164C GLN 2.7 11.1 + - - +
165C ILE* 3.5 19.1 - - + +
166C ILE* 3.1 28.0 + - - +
190C VAL 4.1 0.6 + - - -
191C MET* 1.3 72.7 - - - +
193C VAL* 1.3 92.6 + - - +
194C ALA* 3.9 3.0 - - - +
195C GLU* 3.3 15.4 + - - -
221C VAL* 3.5 15.0 - - + +
223C GLY 3.1 23.6 + - - +
224C PHE 3.6 20.6 - - - -
225C GLY* 4.1 5.2 - - - +
228C ALA* 3.8 17.0 - - + -
229C GLY* 4.1 11.7 - - - +
232C ILE* 3.7 17.7 - - + +
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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
------------------------------------------------------------
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