Contacts of the strand formed by residues 192 - 196 (chain F) in PDB entry 6QY3
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 192 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14F VAL* 5.4 2.8 - - - +
16F LEU 3.0 11.3 + - - +
17F GLY* 4.4 8.3 - - - -
18F THR* 2.9 28.6 + - - -
164F LEU* 3.2 12.8 - - + +
185F THR* 5.4 7.0 - - - -
190F ALA* 3.7 4.9 + - + +
191F ASP* 1.3 73.5 - - - +
193F LEU* 1.3 60.1 - - - +
194F PHE 4.2 0.4 - - - -
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Residues in contact with LEU 193 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F VAL* 5.1 10.3 - - + -
18F THR* 3.4 11.0 - - - +
20F LEU* 6.2 2.2 - - + -
163F ILE* 6.6 0.2 - - + -
164F LEU 3.0 11.2 + - - +
165F VAL* 3.3 11.7 - - + +
166F PHE* 2.9 25.4 + - - +
192F VAL* 1.3 75.1 - - - +
194F PHE* 1.3 62.1 + - - +
195F LEU* 5.5 0.3 - - - +
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Residues in contact with PHE 194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F THR 2.8 15.8 + - - +
19F VAL* 4.3 10.5 - - + -
20F LEU* 2.7 35.8 + - - +
166F PHE* 3.5 14.6 - - + +
169F SER* 6.1 1.8 - - - +
170F LEU* 5.4 13.0 - - + +
192F VAL 4.2 0.4 - - - -
193F LEU* 1.3 73.1 - - - +
195F LEU* 1.3 59.6 + - - +
196F GLU* 4.1 2.2 - - + -
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Residues in contact with LEU 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F LEU* 3.3 8.1 - - + +
166F PHE 3.0 13.5 + - - +
167F VAL* 4.7 5.8 - - + -
168F ASN* 2.7 33.5 + - - +
193F LEU 5.5 0.7 - - - +
194F PHE* 1.3 74.0 - - - +
196F GLU* 1.3 58.7 + - - +
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Residues in contact with GLU 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F LEU 3.0 9.0 + - - +
21F VAL* 3.2 6.7 - - + -
22F ILE* 3.0 24.8 + - - +
28F PHE* 6.2 0.7 - - - -
168F ASN* 4.7 7.6 - - - +
170F LEU* 5.0 16.6 - - + +
194F PHE* 4.1 2.6 - - + -
195F LEU* 1.3 74.4 - - - +
197F PRO* 1.3 62.3 - - - +
198F ARG 3.5 18.3 + - - +
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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