Contacts of the helix formed by residues 315 - 323 (chain D) in PDB entry 7A62
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 SER 315 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188D MET* 4.0 2.2 - - - +
278D GLY* 5.0 7.0 - - - -
313D ASN 3.6 1.2 + - - -
314D PRO* 1.3 74.7 - - - +
316D VAL* 1.3 62.2 + - - +
317D ARG* 3.0 11.6 + - - +
318D GLU* 2.8 46.4 + - - +
319D PHE* 3.3 20.1 + - - +
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Residues in contact with VAL 316 (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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184D VAL* 3.8 13.2 - - + -
185D PHE* 4.2 6.1 - - + -
188D MET* 3.4 32.8 - - + -
196D LEU* 5.2 3.4 - - + -
200D LEU* 4.5 19.7 - - + -
276D LEU* 3.3 37.9 + - + +
277D LEU* 4.9 2.9 - - + -
278D GLY 5.7 0.4 - - - +
314D PRO 3.3 2.4 + - - -
315D SER* 1.3 71.5 - - - +
317D ARG* 1.3 66.8 + - - +
319D PHE* 3.4 3.1 + - - +
320D VAL* 3.3 23.6 + - + +
332D TYR* 4.2 19.1 - - + -
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Residues in contact with ARG 317 (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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277D LEU 3.7 11.0 + - - +
278D GLY* 4.6 11.7 - - - -
315D SER* 3.0 7.5 + - - +
316D VAL* 1.3 78.6 - - - +
318D GLU* 1.3 64.7 + - - +
320D VAL* 2.8 18.9 + - + +
321D LEU* 3.0 30.0 + - + +
332D TYR* 3.1 44.4 + - + +
397D LYS 4.5 3.2 + - - -
398D SER* 2.5 49.1 + - - +
399D LEU 4.5 2.8 + - - -
400D LEU* 3.7 15.4 - - + +
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Residues in contact with GLU 318 (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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314D PRO* 6.0 1.5 - - - +
315D SER* 2.8 33.5 + - - +
317D ARG* 1.3 74.0 - - - +
319D PHE* 1.3 64.6 + - - +
321D LEU* 3.4 12.6 + - - +
322D SER* 3.0 26.2 + - - -
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Residues in contact with PHE 319 (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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187D ALA 5.4 0.2 - - - -
188D MET* 3.2 49.8 - - + -
191D GLN* 4.1 20.0 - - - -
193D ARG* 6.3 2.0 - - - -
196D LEU* 4.0 25.4 - - + -
314D PRO* 6.4 1.3 - - + -
315D SER 3.3 17.6 + - - +
316D VAL 3.4 5.8 - - - +
317D ARG 2.8 1.6 + - - -
318D GLU* 1.3 80.9 - - - +
320D VAL* 1.3 65.3 + - + +
322D SER* 2.6 24.5 + - - -
323D LYS* 3.3 45.4 - - + +
328D LEU* 4.7 4.5 - - + -
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Residues in contact with VAL 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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196D LEU* 4.7 7.2 - - + -
200D LEU* 4.7 3.8 - - + -
316D VAL* 3.4 20.9 - - + +
317D ARG 2.8 16.8 + - - +
319D PHE* 1.3 79.7 - - + +
321D LEU* 1.3 66.5 + - + +
323D LYS* 3.3 13.7 + - - +
324D GLY* 4.0 4.3 + - - -
325D ASP 4.5 5.7 + - - +
328D LEU* 4.0 41.0 - - + +
329D ARG* 4.6 8.0 - - + +
332D TYR* 4.3 17.5 - - + -
400D LEU* 3.7 29.2 - - + -
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Residues in contact with LEU 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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317D ARG* 3.0 54.9 + - + +
318D GLU* 3.6 10.1 - - - +
320D VAL* 1.3 82.4 - - + +
322D SER* 1.3 62.7 + - - +
323D LYS 3.2 0.5 + - - -
324D GLY* 3.7 7.6 + - - -
329D ARG* 5.4 10.2 + - - +
400D LEU* 3.5 29.2 - - + -
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Residues in contact with SER 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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318D GLU* 3.0 16.4 + - - -
319D PHE* 2.6 22.6 + - - -
321D LEU* 1.3 79.6 - - - +
323D LYS* 1.3 79.1 + - - +
324D GLY 3.5 0.9 + - - -
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Residues in contact with LYS 323 (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 GLN* 3.3 34.4 - - - +
319D PHE* 3.3 44.1 - - + +
320D VAL* 3.3 8.4 + - - +
321D LEU 3.1 1.2 - - - -
322D SER* 1.3 96.3 + - - +
324D GLY* 1.3 66.9 + - - +
325D ASP* 3.1 14.4 + - + +
328D LEU* 4.8 7.0 - - + -
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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