Contacts of the strand formed by residues 318 - 322 (chain D) in PDB entry 2VKM
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 ASP 318 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159D PHE* 5.9 2.5 - - - +
160D PRO* 5.9 2.9 - - - +
269D CYS* 3.4 0.7 - - - -
270D TRP* 2.9 32.1 + - - +
271D GLN 5.2 0.2 - - - +
272D ALA* 4.3 1.9 - - - -
273D GLY* 2.9 32.7 + - - +
275D THR* 3.8 10.1 + - - +
316D GLN 4.1 4.5 - - - +
317D ASP* 1.3 75.5 - - - +
319D CYS* 1.3 60.2 + - - +
320D TYR* 3.6 31.6 + - + +
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Residues in contact with CYS 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160D PRO* 5.6 2.8 - - - +
267D LEU* 4.0 12.3 - - + -
268D VAL 3.1 4.5 - - - +
269D CYS* 2.5 44.4 - - - -
308D PRO* 3.5 3.5 - - - +
309D VAL* 3.0 37.3 + - - +
311D ASP* 3.6 30.5 - - - -
317D ASP* 3.8 6.8 + - - -
318D ASP* 1.3 73.7 - - - +
320D TYR* 1.3 70.6 + - - +
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Residues in contact with TYR 320 (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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158D GLY 4.1 18.6 + - - -
261D PHE* 4.5 4.0 - - + -
267D LEU* 3.1 6.8 - - - -
268D VAL* 2.8 33.1 + - - +
270D TRP* 3.7 21.8 - + + -
275D THR* 3.0 33.2 + - + -
277D TRP* 3.3 31.8 + + - -
306D LEU* 3.7 31.6 - - + -
307D ARG 3.0 8.1 - - - +
308D PRO* 3.7 16.8 - - + -
309D VAL* 4.1 2.5 - - - -
318D ASP* 3.6 29.6 + - + +
319D CYS* 1.3 81.7 - - - +
321D LYS* 1.3 62.8 + - - +
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Residues in contact with LYS 321 (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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261D PHE* 4.5 2.2 - - - -
264D GLY* 4.1 21.7 + - - +
265D GLU 4.5 11.9 + - - -
266D GLN* 4.6 3.1 - - - +
267D LEU* 4.0 25.6 - - + +
306D LEU* 3.5 3.5 - - - -
307D ARG* 2.9 38.6 + - + +
309D VAL* 4.0 21.3 - - + +
320D TYR* 1.3 78.4 - - - +
322D PHE* 1.3 67.6 + - - +
323D ALA* 3.3 0.9 + - + -
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Residues in contact with PHE 322 (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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233D ASN* 4.9 3.1 + - - -
245D VAL* 4.2 14.1 - - + -
248D ILE* 4.3 10.3 - - + -
261D PHE* 3.3 41.4 + + + +
262D TRP* 3.3 54.1 - + - -
264D GLY* 3.8 18.3 - - - -
266D GLN 5.2 0.2 + - - -
280D PHE* 6.2 0.4 - + - -
305D TYR* 3.9 25.1 - + - -
306D LEU* 4.0 17.0 - - + -
321D LYS* 1.3 72.5 - - - +
323D ALA* 1.3 59.1 + - - +
324D ILE* 3.3 50.5 + - + +
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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