Contacts of the helix formed by residues 317 - 328 (chain A) in PDB entry 4WB7
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 317 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195A GLU* 2.7 37.1 + - - -
315A HIS 3.4 1.7 + - - -
316A PHE* 1.3 75.6 - - - +
318A SER* 1.3 64.1 + - - +
319A ASP* 3.8 5.7 + - - +
320A LEU* 3.1 16.7 + - - +
321A LYS* 3.1 22.3 + - - +
351A TRP* 4.0 4.0 - - - -
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Residues in contact with SER 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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316A PHE 3.9 0.6 + - - -
317A SER* 1.3 73.5 - - - +
319A ASP* 1.3 66.0 + - - +
321A LYS* 3.4 18.1 + - - +
322A ASP* 3.0 23.6 + - - +
325A ARG* 5.1 1.0 + - - -
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Residues in contact with ASP 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A SER* 3.2 5.5 + - - +
318A SER* 1.3 76.6 - - - +
320A LEU* 1.3 66.2 + - - +
322A ASP* 3.3 3.5 + - - +
323A LEU* 3.0 19.9 + - - +
349A HIS* 3.2 14.0 - - + -
350A LYS* 3.5 42.3 + - + +
351A TRP* 4.0 25.5 - - + +
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Residues in contact with LEU 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A GLU* 3.6 27.8 - - + +
283A ILE* 3.7 27.6 - - + -
287A ALA* 3.8 22.2 - - + -
316A PHE* 3.8 22.7 - - + -
317A SER* 3.1 23.7 + - - +
319A ASP* 1.3 77.4 - - - +
321A LYS* 1.3 57.1 + - - +
323A LEU* 3.2 4.9 + - + +
324A LEU* 2.9 47.5 + - + +
351A TRP* 3.6 25.7 - - + +
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Residues in contact with LYS 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A PHE* 3.7 40.7 - - + -
313A PRO 5.0 2.3 + - - +
314A SER* 5.8 3.4 + - - +
316A PHE* 3.7 27.2 + - + +
317A SER 3.1 17.9 + - - +
318A SER* 3.8 16.6 + - - +
319A ASP 3.3 0.2 - - - -
320A LEU* 1.3 76.5 - - - +
322A ASP* 1.3 59.2 + - - +
324A LEU* 3.3 1.9 + - - +
325A ARG* 2.9 59.8 + - - +
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Residues in contact with ASP 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A SER 3.0 17.4 + - - +
319A ASP* 3.8 5.8 - - - +
320A LEU 3.2 0.2 - - - -
321A LYS* 1.3 78.0 - - - +
323A LEU* 1.3 62.8 + - - +
325A ARG* 3.4 17.1 + - - +
326A ASN* 2.9 41.8 + - - -
336A PHE* 5.7 0.2 - - - -
349A HIS* 2.8 26.7 + - + +
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Residues in contact with LEU 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A ILE* 4.2 16.2 - - + -
319A ASP 3.0 16.5 + - - +
320A LEU* 3.2 8.3 + - + +
322A ASP* 1.3 76.6 - - - +
324A LEU* 1.3 59.7 + - + +
326A ASN* 3.1 5.1 + - - +
327A LEU* 3.0 42.3 + - + +
336A PHE* 4.4 12.1 - - + -
346A ILE* 4.6 10.5 - - + -
349A HIS* 3.5 34.5 + - + +
351A TRP* 3.5 34.8 - - + -
352A PHE* 3.8 13.9 - - + -
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Residues in contact with LEU 324 (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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280A GLY* 3.4 36.8 - - - +
283A ILE* 4.0 15.9 - - + -
284A TYR* 4.0 14.4 - - + -
312A PHE* 3.7 24.0 - - + -
316A PHE* 3.6 31.6 - - + -
320A LEU* 2.9 33.6 + - + +
321A LYS 3.8 0.4 - - - +
323A LEU* 1.3 76.1 - - + +
325A ARG* 1.3 59.7 + - - +
327A LEU* 4.3 6.7 - - + +
328A LEU* 2.8 41.2 + - + +
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Residues in contact with ARG 325 (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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312A PHE* 3.8 33.8 - - + -
318A SER 5.1 1.0 + - - -
321A LYS* 2.9 54.5 + - - +
322A ASP* 3.8 17.1 + - - +
323A LEU 3.3 0.2 - - - -
324A LEU* 1.3 76.5 - - - +
326A ASN* 1.3 63.3 + - - +
328A LEU* 3.9 3.4 - - - +
329A GLN* 3.8 25.1 + - - +
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Residues in contact with ASN 326 (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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322A ASP* 2.9 39.6 + - - +
323A LEU 3.1 8.3 + - - +
325A ARG* 1.3 82.1 - - - +
327A LEU* 1.3 62.7 + - - +
329A GLN* 3.5 16.1 + - - +
334A LYS 4.8 4.9 - - - +
335A ARG* 3.6 0.9 - - - -
336A PHE* 3.0 69.9 + - + -
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Residues in contact with LEU 327 (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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276A TRP* 3.8 15.7 - - + +
277A TRP* 3.7 9.7 - - - -
279A LEU* 4.2 8.7 - - + -
280A GLY* 3.8 31.0 - - - +
283A ILE* 4.0 17.3 - - + -
323A LEU* 3.0 39.5 + - + +
324A LEU* 4.1 4.7 - - + +
326A ASN* 1.3 75.2 - - - +
328A LEU* 1.3 58.3 + - - +
329A GLN 3.0 9.5 + - - -
335A ARG* 3.3 23.5 + - - -
336A PHE* 3.8 29.4 - - + +
346A ILE* 4.0 17.9 - - + -
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Residues in contact with LEU 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A TRP* 3.3 41.8 - - + +
280A GLY* 3.8 14.4 - - - +
281A VAL* 3.6 34.1 - - + +
284A TYR* 4.5 7.4 - - + -
292A PRO* 4.2 25.8 - - + -
293A PHE* 4.7 1.1 - - + -
308A GLY 4.8 6.6 - - - +
310A VAL* 4.3 25.0 - - + +
312A PHE* 5.3 0.4 - - + -
324A LEU* 2.8 28.7 + - + +
325A ARG* 3.9 7.6 - - - +
327A LEU* 1.3 68.1 - - - +
329A GLN* 1.3 60.7 + - - +
330A VAL* 3.5 4.7 + - - +
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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