Contacts of the helix formed by residues 314 - 318 (chain C) in PDB entry 2EWY
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 LEU 314 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295C LYS* 3.3 46.2 - - + +
312C THR* 4.7 2.5 - - + -
313C ILE* 1.3 80.3 - - - +
315C PRO* 1.3 75.6 - - + +
316C GLN* 3.1 17.0 - - - +
317C LEU* 2.9 17.3 + - - +
318C TYR* 3.8 5.5 - - - -
378C ALA 3.3 26.7 - - - +
379C VAL* 2.9 24.9 + - + +
380C SER* 4.4 1.3 - - - +
381C GLU* 4.2 14.1 - - + +
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Residues in contact with PRO 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C TRP* 3.5 33.9 - - + +
293C PHE* 3.6 29.6 - - + +
294C PRO 3.9 15.5 - - - +
295C LYS* 4.8 1.8 - - + -
314C LEU* 1.3 83.8 - - + +
316C GLN* 1.3 73.5 + - - +
317C LEU 2.9 2.7 - - - -
318C TYR* 3.5 16.5 - - + -
319C ILE* 2.8 31.8 + - + +
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Residues in contact with GLN 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C ALA* 5.4 6.0 - - + +
290C TRP* 3.3 57.0 - - + +
314C LEU* 3.0 13.6 + - - +
315C PRO* 1.3 93.0 - - - +
317C LEU* 1.3 63.2 + - + +
319C ILE 4.1 8.8 - - - +
320C GLN* 4.6 5.0 - - - +
321C PRO* 4.7 2.9 - - - +
374C ILE* 4.6 19.2 + - + +
377C ALA* 5.9 4.4 - - - +
378C ALA 5.6 1.2 + - - -
379C VAL* 3.2 26.4 - - + +
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Residues in contact with LEU 317 (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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172C GLY 4.9 9.2 - - - +
173C ALA* 5.0 7.0 - - + -
313C ILE* 3.5 29.8 - - + -
314C LEU 2.9 8.4 + - - +
315C PRO 2.9 0.8 - - - -
316C GLN* 1.3 83.4 - - + +
318C TYR* 1.3 59.0 + - - +
319C ILE 3.7 0.4 - - - -
320C GLN* 3.2 24.8 + - - +
348C THR* 3.8 19.4 + - - +
351C GLU* 4.8 17.5 - - + +
352C GLY* 3.8 21.5 - - - +
372C ALA* 5.7 0.2 - - + -
379C VAL* 3.6 48.5 - - + +
380C SER* 4.3 0.9 - - - -
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Residues in contact with TYR 318 (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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261C VAL* 3.8 16.2 - - + +
293C PHE* 3.5 3.2 - + - +
294C PRO* 2.7 48.4 + - - +
296C ILE* 3.4 34.3 - - + +
313C ILE* 4.0 19.7 - - + -
314C LEU 3.8 6.3 - - - -
315C PRO* 3.0 26.1 + - + -
317C LEU* 1.3 77.9 - - - +
319C ILE* 1.3 83.1 + - + +
320C GLN* 3.4 4.3 - - - -
334C PHE* 3.7 14.8 - + - -
335C GLY* 2.7 29.5 + - - -
336C ILE* 4.3 13.7 - - + -
348C THR* 4.5 4.5 - - - +
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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