Contacts of the strand formed by residues 207 - 212 (chain D) 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 207 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203D HIS* 4.8 7.0 - - + -
205D GLY 3.1 6.1 + - - +
206D TRP* 1.3 75.3 - - - +
208D ARG* 1.3 60.4 + - - +
209D CYS 6.0 0.2 - - - +
221D THR* 5.9 4.0 - - - -
222D GLY 3.5 12.6 - - - +
223D SER* 3.8 6.7 - - - +
466D PHE* 4.5 8.3 - - - +
480D ALA* 4.5 18.9 - - + +
481D GLU 3.8 15.3 + - - +
482D ALA* 5.2 0.9 - - - -
484D LYS* 4.5 20.4 - - - +
485D THR 5.0 2.0 - - - +
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Residues in contact with ARG 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206D TRP 4.3 6.1 - - - +
207D VAL* 1.3 75.9 - - - +
209D CYS* 1.3 61.8 + - - +
222D GLY 3.2 8.0 + - - +
223D SER 5.5 0.2 - - - -
249D VAL 3.3 25.8 - - - +
250D ARG* 4.5 9.6 - - - +
466D PHE* 3.0 33.0 - - + +
467D ALA* 3.4 5.9 - - - +
480D ALA* 5.1 1.5 - - - +
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Residues in contact with CYS 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208D ARG* 1.3 80.3 + - + +
210D ILE* 1.3 61.4 + - - +
221D THR* 3.3 29.0 - - - -
222D GLY* 3.7 5.9 + - - +
249D VAL 5.4 0.7 - - - +
250D ARG 4.4 5.6 - - - +
251D GLY* 4.1 12.8 - - - +
252D VAL* 4.0 30.5 - - + +
467D ALA* 3.8 6.3 - - - -
480D ALA* 5.0 3.9 - - - +
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Residues in contact with ILE 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209D CYS* 1.3 75.5 - - - +
211D ALA* 1.3 63.2 + - - +
219D PHE* 6.3 1.1 - - + -
220D VAL 3.8 4.5 - - - +
221D THR* 4.8 2.7 - - - -
252D VAL 4.5 4.4 - - - +
467D ALA* 3.7 18.4 - - + +
468D CYS 4.9 3.4 - - - +
469D ALA* 4.5 24.2 - - + +
478D LEU 5.1 5.6 - - - +
479D THR 6.0 0.2 - - - -
480D ALA* 5.1 6.1 - - + +
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Residues in contact with ALA 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209D CYS 4.4 0.2 - - - -
210D ILE* 1.3 75.2 - - - +
212D VAL* 1.3 62.3 + - - +
219D PHE* 3.2 7.3 - - - +
220D VAL* 2.9 40.0 + - + +
252D VAL* 3.4 23.7 + - - +
253D ILE* 3.7 17.0 - - + -
254D VAL* 4.2 7.2 - - + +
469D ALA* 5.7 2.5 - - - -
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Residues in contact with VAL 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211D ALA* 1.3 78.0 - - - +
213D GLU* 1.3 70.3 + - - +
214D PRO 3.8 0.2 - - - -
218D TRP 4.1 2.0 - - - +
219D PHE* 3.9 18.6 - - + +
254D VAL* 4.8 11.7 + - - +
469D ALA* 5.7 4.9 - - + -
470D PHE 4.7 14.4 - - - +
471D ASP* 5.8 2.9 - - - -
472D GLN 6.0 1.8 - - - +
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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