Contacts of the strand formed by residues 283 - 288 (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 ILE 283 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206D VAL* 4.9 3.4 - - + -
207D GLU 3.6 8.1 - - - +
208D ILE* 4.0 17.7 - - + -
234D LEU* 5.0 7.6 - - + -
244D ALA* 6.4 0.2 - - + -
248D ILE* 4.0 15.0 - - + -
281D PRO 4.3 1.8 - - - +
282D VAL* 1.3 80.1 - - - +
284D SER* 1.3 69.2 + - - +
285D LEU* 4.2 14.3 + - + +
298D ILE 3.8 1.0 - - - +
299D THR* 3.3 1.5 - - - -
300D ILE* 2.9 49.2 + - + +
305D TYR* 3.5 23.3 - - + -
324D ILE* 3.4 32.3 - - + -
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Residues in contact with SER 284 (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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205D ARG 3.9 0.3 - - - +
206D VAL* 3.4 6.8 - - - +
207D GLU* 3.0 48.7 + - - +
210D GLY 5.7 1.2 + - - -
282D VAL* 4.3 3.7 - - - +
283D ILE* 1.3 71.4 - - - +
285D LEU* 1.3 66.3 + - - +
286D TYR* 4.2 14.3 - - - -
297D ARG* 4.2 9.0 + - - -
298D ILE 3.3 4.7 - - - -
299D THR* 2.6 28.6 + - - +
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Residues in contact with LEU 285 (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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203D ILE* 4.3 28.0 - - + -
205D ARG 3.7 2.2 - - - +
206D VAL* 3.8 31.2 - - + -
234D LEU* 4.7 13.7 - - + -
236D LEU* 5.4 7.4 - - + -
283D ILE* 4.2 12.8 + - + +
284D SER* 1.3 77.5 - - - +
286D TYR* 1.3 63.5 + - - +
287D LEU* 3.8 4.8 + - + +
297D ARG* 3.2 0.9 - - - -
298D ILE* 2.9 44.5 + - + +
333D MET* 4.3 20.2 - - + -
337D ILE* 3.9 27.4 - - + -
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Residues in contact with TYR 286 (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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365A PHE* 3.4 10.8 - + - -
203D ILE* 3.3 7.5 - - - +
204D VAL* 2.9 43.0 + - + -
205D ARG* 2.9 41.6 + - + +
207D GLU* 2.4 40.5 + - + -
284D SER* 4.2 7.6 - - - -
285D LEU* 1.3 76.6 - - - +
287D LEU* 1.3 60.7 + - - +
295D SER* 4.0 8.5 - - - +
296D PHE 3.1 5.6 - - - +
297D ARG* 2.9 44.9 + - + -
374D PHE* 3.7 40.4 - + + -
376D THR* 5.6 2.0 - - + -
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Residues in contact with LEU 287 (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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191D THR* 3.8 7.9 - - + +
201D VAL* 4.1 22.0 - - + -
202D ILE 3.6 15.3 - - - +
203D ILE* 4.1 20.4 - - + -
204D VAL* 4.6 0.7 - - - -
285D LEU* 4.5 7.0 - - + +
286D TYR* 1.3 76.2 - - - +
288D MET* 1.3 66.0 + - - +
289D GLY 3.3 0.2 + - - -
295D SER* 3.4 4.1 - - - -
296D PHE* 2.7 59.6 + - + -
298D ILE* 4.2 15.3 - - + -
333D MET* 4.6 5.6 - - + -
354D PHE* 3.5 37.2 - - + -
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Residues in contact with MET 288 (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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190D TYR 3.9 0.2 - - - +
191D THR* 2.7 34.7 + - - +
192D PRO* 3.2 17.0 - - + +
202D ILE* 3.3 39.9 + - + +
204D VAL* 4.2 7.8 - - + +
287D LEU* 1.3 72.0 - - - +
289D GLY* 1.3 69.0 + - - +
294D GLN 4.3 1.3 - - - -
295D SER* 4.4 5.4 - - - -
296D PHE* 3.9 0.5 - - - -
379D MET* 3.2 55.9 - - + +
380D GLU* 3.6 11.7 - - + +
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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