Contacts of the strand formed by residues 196 - 201 (chain F) in PDB entry 6FF7
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 196 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155F ASN* 3.5 17.7 - - - +
170F GLY* 4.1 6.9 - - - -
171F SER 3.2 30.8 + - - +
174F GLY 5.0 4.7 - - - +
175F THR 4.5 9.9 - - - +
176F VAL* 5.8 3.1 - - + -
192F ASN* 6.0 2.9 - - + -
194F TYR 3.4 4.5 + - - +
195F GLN* 1.3 73.8 - - - +
197F LEU* 1.3 60.8 + - - +
198F ALA 5.2 1.6 - - - +
210F SER* 5.7 8.3 - - - -
211F GLY 4.1 6.7 - - - +
212F GLY* 4.2 2.5 - - - -
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Residues in contact with LEU 197 (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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155F ASN* 3.9 14.0 - - + +
156F SER* 3.5 17.3 - - - -
170F GLY* 6.4 0.7 - - - -
195F GLN 3.9 1.8 + - - +
196F VAL* 1.3 75.8 - - - +
198F ALA* 1.3 57.8 + - - +
211F GLY 2.9 10.9 + - - +
212F GLY* 4.8 4.5 - - - +
238F VAL 3.4 24.0 - - - +
239F THR* 4.5 10.0 - - - +
288F LEU* 6.5 0.9 - - + -
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Residues in contact with ALA 198 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156F SER* 4.2 6.7 - - - -
196F VAL* 3.9 1.6 - - - +
197F LEU* 1.3 80.7 - - + +
199F VAL* 1.3 61.0 + - - +
209F ILE 3.8 0.5 - - - +
210F SER* 3.4 3.3 - - - -
211F GLY* 2.8 38.2 + - - +
238F VAL* 4.9 1.8 - - + +
239F THR 3.9 4.7 - - - +
240F GLY* 3.8 15.5 - - - +
241F LEU* 3.8 31.4 - - + +
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Residues in contact with VAL 199 (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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156F SER* 4.5 11.5 - - - +
157F CYS 4.6 3.3 - - - +
158F TYR* 3.4 20.0 + - - +
168F CYS* 5.0 20.0 - - + +
169F THR 5.2 11.0 - - - +
170F GLY* 5.4 3.1 - - - +
198F ALA* 1.3 76.9 - - - +
200F THR* 1.3 62.7 + - - +
208F ILE* 6.3 1.8 - - + -
209F ILE 3.2 9.6 - - - +
210F SER* 4.8 7.0 - - - -
241F LEU* 5.2 2.8 + - - +
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Residues in contact with THR 200 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158F TYR* 4.1 8.7 - - - -
168F CYS* 6.1 3.1 - - - -
199F VAL* 1.3 77.0 - - - +
201F PHE* 1.3 64.1 + - - +
208F ILE* 3.7 2.7 - - - -
209F ILE* 2.8 46.2 + - - +
241F LEU* 4.6 22.4 - - - +
242F SER* 5.0 0.7 - - - -
243F LEU* 4.9 14.6 - - - -
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Residues in contact with PHE 201 (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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158F TYR* 4.6 7.6 - - + +
159F PRO 5.7 1.3 - - - -
160F ALA* 4.7 25.1 - - + +
200F THR* 1.3 75.0 - - - +
202F ASN* 1.3 71.3 + - - +
205F SER* 5.1 4.5 - - - -
207F GLN 3.4 11.0 - - - +
208F ILE* 4.8 1.1 - - - +
209F ILE* 5.9 0.4 - - - -
243F LEU* 4.4 15.1 - - - +
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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