Contacts of the helix formed by residues 315 - 323 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188A MET* 4.4 2.1 - - - +
278A GLY* 5.0 7.4 - - - -
313A ASN 3.6 2.1 + - - -
314A PRO* 1.3 75.3 - - - +
316A VAL* 1.3 61.7 + - - +
317A ARG* 3.1 12.3 + - - +
318A GLU* 3.0 38.1 + - - +
319A PHE* 3.2 20.1 + - - +
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Residues in contact with VAL 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A VAL* 3.8 19.7 - - + -
185A PHE* 4.2 14.4 - - + -
188A MET* 3.7 25.6 - - - -
196A LEU* 5.3 2.7 - - + -
200A LEU* 4.6 18.2 - - + -
276A LEU* 3.6 29.3 + - + +
277A LEU* 4.9 2.9 - - + -
278A GLY 6.0 0.2 - - - +
314A PRO 3.4 1.2 + - - -
315A SER* 1.3 71.6 - - - +
317A ARG* 1.3 59.0 + - - +
319A PHE* 3.2 2.5 + - + +
320A VAL* 2.9 34.6 + - + +
332A TYR* 4.2 20.0 - - + -
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Residues in contact with ARG 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A LEU 3.7 13.2 + - - +
278A GLY* 4.4 13.8 + - - -
315A SER* 3.1 8.1 + - - +
316A VAL* 1.3 79.5 - - - +
318A GLU* 1.3 70.4 + - - +
320A VAL* 3.2 2.6 + - - +
321A LEU* 2.9 43.5 + - + +
332A TYR* 3.0 38.8 + - + +
397A LYS 5.0 2.0 + - - -
398A SER* 2.7 44.8 + - - +
399A LEU 4.8 2.4 + - - -
400A LEU* 3.7 17.9 - - + +
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Residues in contact with GLU 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A SER* 3.0 27.8 + - - +
317A ARG* 1.3 85.5 + - - +
319A PHE* 1.3 57.7 + - - +
321A LEU* 3.4 19.8 + - - +
322A SER* 2.8 32.7 + - - -
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Residues in contact with PHE 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A ALA 5.2 0.2 - - - -
188A MET* 3.9 46.4 - - + -
191A GLN* 4.0 17.9 - - - -
192A GLU 5.9 0.7 - - - -
193A ARG* 6.1 3.4 - - - -
196A LEU* 3.5 33.0 - - + -
315A SER 3.2 14.8 + - - +
316A VAL 3.4 9.2 - - - +
317A ARG 3.1 0.4 - - - -
318A GLU* 1.3 78.6 - - - +
320A VAL* 1.3 64.8 + - + +
322A SER* 2.7 22.1 + - - -
323A LYS* 3.2 48.9 - - + +
328A LEU* 4.4 5.4 - - + -
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Residues in contact with VAL 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A LEU* 5.0 2.2 - - + -
200A LEU* 4.6 8.1 - - + -
316A VAL* 2.9 27.2 + - + +
317A ARG 3.9 3.1 - - - +
319A PHE* 1.3 81.4 - - + +
321A LEU* 1.3 62.9 + - - +
322A SER 3.3 0.5 + - - -
323A LYS* 3.4 10.6 + - - +
324A GLY 4.1 4.3 + - - -
325A ASP 4.7 2.1 + - - -
328A LEU* 3.6 25.1 - - + +
329A ARG* 3.6 46.0 - - + +
332A TYR* 4.1 21.5 - - + -
400A LEU* 3.9 10.1 - - + -
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Residues in contact with LEU 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317A ARG* 2.9 48.9 + - + +
318A GLU* 4.1 18.8 - - - +
320A VAL* 1.3 76.9 - - - +
322A SER* 1.3 61.2 + - - +
323A LYS 3.3 0.3 + - - -
324A GLY* 4.0 6.6 + - - -
329A ARG* 4.9 9.6 - - - +
400A LEU* 3.5 32.3 - - + -
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Residues in contact with SER 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A GLU 2.8 16.4 + - - -
319A PHE* 2.7 24.2 + - - -
321A LEU* 1.3 77.9 - - - +
323A LYS* 1.3 72.3 + - - +
324A GLY 3.5 1.2 + - - -
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Residues in contact with LYS 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A GLN* 2.6 39.1 + - - +
319A PHE* 3.2 49.1 - - + +
320A VAL 3.4 5.7 + - - +
321A LEU 3.2 1.4 - - - -
322A SER* 1.3 86.6 - - - +
324A GLY* 1.3 66.0 + - - +
325A ASP* 3.1 16.1 + - + +
328A LEU* 4.5 7.6 - - + -
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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