Contacts of the strand formed by residues 383 - 388 (chain D) in PDB entry 6OVR
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 GLY 383 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213D VAL* 4.1 4.7 - - - -
214D GLU 3.1 14.4 - - - -
215D TYR* 3.8 3.1 - - - -
216D VAL* 4.1 4.0 - - - -
359D ALA 3.6 1.7 - - - +
360D ARG* 3.8 3.1 - - - +
361D VAL* 3.0 38.1 + - - +
381D ALA 3.4 2.5 + - - -
382D GLU* 1.3 81.3 - - - +
384D VAL* 1.3 60.5 + - - -
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Residues in contact with VAL 384 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212D ARG 3.8 0.3 - - - +
213D VAL* 3.1 2.7 - - - +
214D GLU* 2.8 46.0 + - + +
340D THR* 6.0 2.9 - - + -
358D GLY* 3.8 21.8 - - - +
359D ALA 3.4 14.6 - - - +
360D ARG* 5.2 2.7 - - + -
383D GLY* 1.3 73.2 - - - -
385D VAL* 1.3 64.6 + - - +
386D HIS* 3.5 23.2 - - + +
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Residues in contact with VAL 385 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211D VAL* 5.0 7.2 - - + -
212D ARG 3.7 3.8 - - - +
213D VAL* 3.7 19.3 - - + -
355D VAL* 4.0 20.2 - - + -
356D PRO 3.0 28.3 - - - +
357D GLU* 4.1 0.7 - - - +
358D GLY* 2.8 29.9 + - - +
359D ALA* 3.2 24.7 - - + +
361D VAL* 4.4 11.7 - - + -
367D ILE* 4.4 9.4 - - + -
384D VAL* 1.3 78.9 - - - +
386D HIS* 1.3 68.0 + - - +
387D LEU* 4.8 2.2 - - + -
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Residues in contact with HIS 386 (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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180D LYS* 5.1 4.8 + - - -
211D VAL* 3.8 7.6 - - - +
212D ARG* 2.9 43.2 + - + +
214D GLU* 4.0 16.2 - - + +
357D GLU* 3.3 15.8 + - - +
358D GLY* 6.1 1.6 - - - -
384D VAL* 3.5 29.5 - - + +
385D VAL* 1.3 82.2 + - - +
387D LEU* 1.3 63.6 + - - +
388D HIS* 3.7 22.8 + - + +
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Residues in contact with LEU 387 (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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180D LYS* 3.6 14.0 + - - -
181D ASP* 5.6 1.8 - - + -
205D TYR* 4.2 23.8 + - + -
208D PRO* 3.4 33.9 - - + -
210D ARG 4.1 0.4 - - - -
211D VAL* 4.6 13.0 - - + -
353D VAL* 4.3 19.3 - - + -
355D VAL* 4.5 2.9 - - + +
356D PRO 3.9 6.7 - - - +
357D GLU* 3.0 58.5 + - + +
385D VAL* 4.8 3.1 - - + -
386D HIS* 1.3 79.9 - - - +
388D HIS* 1.3 65.9 + - - +
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Residues in contact with HIS 388 (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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176D ASP* 2.9 22.3 + - - -
180D LYS* 3.1 28.9 + - - -
205D TYR* 5.0 1.1 + - - -
208D PRO* 3.1 11.6 - - - +
210D ARG* 3.0 59.7 + - + +
212D ARG* 4.1 21.7 + - + +
386D HIS* 3.7 27.3 + - + +
387D LEU* 1.3 78.2 - - - +
389D GLU* 1.3 74.2 - - - +
390D PRO* 3.5 3.6 - - - -
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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