Contacts of the strand formed by residues 283 - 288 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206C VAL* 4.9 2.9 - - + -
207C GLU 3.5 9.0 - - - +
208C ILE* 4.0 17.0 - - + -
234C LEU* 5.0 7.2 - - + -
244C ALA* 6.3 0.4 - - + -
248C ILE* 3.8 15.7 - - + -
281C PRO 4.2 2.2 - - - +
282C VAL* 1.3 80.6 - - - +
284C SER* 1.3 66.9 + - - +
285C LEU* 4.3 15.9 + - + +
298C ILE 3.7 0.9 - - - +
299C THR* 3.2 2.1 - - - -
300C ILE* 2.8 47.6 + - + +
305C TYR* 3.6 24.7 - - + +
324C ILE* 3.5 33.0 - - + -
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Residues in contact with SER 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205C ARG 4.0 0.2 - - - +
206C VAL* 3.4 5.9 - - - +
207C GLU* 3.0 53.8 + - - +
210C GLY 5.7 1.2 + - - -
282C VAL* 4.9 3.5 - - - +
283C ILE* 1.3 73.2 - - - +
285C LEU* 1.3 66.0 + - - +
286C TYR* 4.4 3.8 - - - -
297C ARG* 4.3 16.0 + - - -
298C ILE 3.1 5.4 - - - -
299C THR* 2.6 30.7 + - - +
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Residues in contact with LEU 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C ILE* 4.1 28.7 - - + -
205C ARG 3.8 2.2 - - - -
206C VAL* 3.9 27.6 - - + -
234C LEU* 4.9 12.6 - - + -
236C LEU* 5.6 6.3 - - + -
283C ILE* 4.6 12.6 - - + +
284C SER* 1.3 80.8 - - - +
286C TYR* 1.3 63.3 + - - +
287C LEU* 3.9 5.2 + - + +
297C ARG* 3.2 1.1 - - - -
298C ILE* 2.8 44.9 + - + +
331C THR* 5.5 0.2 - - + -
333C MET* 4.3 19.5 - - + -
337C ILE* 4.1 26.5 - - + -
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Residues in contact with TYR 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365B PHE* 3.3 12.1 - + - -
203C ILE* 3.2 8.1 - - - +
204C VAL* 2.8 36.2 + - + -
205C ARG* 2.9 49.7 + - + +
207C GLU* 2.5 41.5 + - + -
284C SER* 4.4 6.7 - - - -
285C LEU* 1.3 76.3 - - - +
287C LEU* 1.3 61.1 + - - +
295C SER* 4.1 9.0 - - - +
296C PHE 3.1 6.7 - - - +
297C ARG* 2.9 40.3 + - + -
374C PHE* 3.5 38.4 - + + -
376C THR* 5.7 0.4 - - - -
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Residues in contact with LEU 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191C THR* 3.6 14.4 - - + +
201C VAL* 4.1 17.0 - - + -
202C ILE 3.5 13.9 - - - +
203C ILE* 3.8 23.1 - - + -
204C VAL* 4.6 0.9 - - - -
285C LEU* 4.5 8.3 - - + +
286C TYR* 1.3 77.7 - - - +
288C MET* 1.3 66.1 + - - +
295C SER* 3.1 7.2 - - - -
296C PHE* 2.8 51.9 + - + -
298C ILE* 4.4 13.2 - - + -
333C MET* 4.6 7.0 - - + -
354C PHE* 3.5 36.1 - - + -
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Residues in contact with MET 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191C THR* 2.6 35.4 + - - +
192C PRO* 3.3 16.6 - - + +
202C ILE* 3.3 44.8 + - + +
204C VAL* 4.5 3.7 - - + +
287C LEU* 1.3 73.8 - - - +
289C GLY* 1.3 69.8 + - - +
294C GLN 4.2 2.2 - - - -
295C SER* 4.3 3.8 - - - -
296C PHE* 3.8 0.5 - - - -
379C MET* 3.5 59.5 - - + +
380C GLU* 3.7 7.2 - - - +
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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