Contacts of the helix formed by residues 316 - 325 (chain B) in PDB entry 2W7P
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 ASN 316 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B ILE* 3.9 9.4 - - - -
314B ALA* 2.7 10.4 + - - +
315B PRO* 1.3 79.9 - - - +
317B THR* 1.3 58.0 + - - +
318B MET* 3.2 23.2 - - - +
319B LEU* 2.9 53.7 - - - +
320B ALA* 3.1 27.9 + - - +
401B GLY 3.8 5.6 - - - +
403B GLY* 2.9 39.9 - - - +
404B SER 3.4 6.3 - - - -
405B THR* 3.7 1.1 - - + -
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Residues in contact with THR 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B ILE* 4.2 13.9 - - + -
201B TYR* 3.7 45.7 - - + -
316B ASN* 1.3 70.4 - - - +
318B MET* 1.3 69.1 + - - +
320B ALA* 3.4 4.0 + - - +
321B LYS* 3.0 25.8 + - - +
404B SER* 2.9 43.3 + - - +
407B LEU* 4.3 14.1 - - + +
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Residues in contact with MET 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B TYR* 5.3 1.1 - - - -
316B ASN* 3.2 12.7 - - - +
317B THR* 1.3 83.4 + - - +
319B LEU* 1.3 89.7 + - + +
321B LYS* 3.5 9.1 + - - +
322B VAL* 3.4 17.3 + - - +
346B ILE* 5.2 2.7 - - + -
349B LEU* 6.4 0.2 - - - -
354B VAL* 4.6 22.0 - - + -
355B SER* 5.3 13.5 + - - +
394B TYR* 6.4 1.8 - - + -
398B ILE* 4.3 26.9 - - + +
401B GLY* 3.5 29.4 - - - +
402B LEU 3.2 24.2 - - - +
403B GLY* 4.1 9.2 - - - -
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Residues in contact with LEU 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314B ALA* 3.6 13.7 - - + -
315B PRO* 4.7 3.4 - - + -
316B ASN* 2.9 35.1 - - - +
318B MET* 1.3 87.8 - - + +
320B ALA* 1.3 65.8 + - - +
322B VAL* 2.9 23.5 + - + +
323B CYS* 3.2 8.4 + - - -
335B ILE* 4.6 9.9 - - + -
342B VAL* 3.4 37.0 - - + -
345B PHE* 3.7 30.1 - - + -
346B ILE* 4.7 13.7 - - + -
349B LEU* 5.3 1.8 - - + -
401B GLY* 3.9 7.6 - - - +
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Residues in contact with ALA 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B ILE* 4.3 13.2 - - + +
105B HIS* 4.2 13.9 - - + -
201B TYR* 5.0 0.2 - - + -
312B GLY* 4.1 16.5 - - - +
314B ALA* 3.4 13.1 - - + +
316B ASN 3.1 19.3 + - - +
317B THR* 3.4 7.2 - - - +
319B LEU* 1.3 78.0 - - - +
321B LYS* 1.3 55.8 + - - +
323B CYS* 2.6 32.0 + - - +
324B SER* 3.2 9.4 + - - -
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Residues in contact with LYS 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B HIS* 3.2 33.5 + - + +
195B MET* 5.8 1.6 - - - +
199B GLU* 2.9 35.0 + - - -
201B TYR* 3.7 17.5 - - + +
317B THR 3.0 14.6 + - - +
318B MET* 3.7 7.6 - - - +
320B ALA* 1.3 75.4 - - - +
322B VAL* 1.3 58.8 + - + +
324B SER* 2.6 21.9 + - - -
325B ASP* 3.6 6.8 - - - +
355B SER* 5.0 21.5 - - - +
1522B CA 3.7 11.7 - - - -
12E T 4.1 3.5 + - - -
13E C 2.8 30.7 + - - -
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Residues in contact with VAL 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318B MET* 3.4 18.4 - - - +
319B LEU* 2.9 11.6 + - + +
320B ALA 2.7 3.8 + - - -
321B LYS* 1.3 77.1 - - + +
323B CYS* 1.3 61.9 + - - +
325B ASP* 3.5 12.5 + - - +
326B LYS* 3.6 9.2 + - - +
345B PHE* 3.9 22.8 - - + -
349B LEU* 4.4 13.7 - - + -
353B LYS* 3.8 21.5 - - + +
354B VAL* 3.7 29.8 - - + -
355B SER 5.5 0.2 - - - +
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Residues in contact with CYS 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311B ALA 4.4 1.0 - - - +
312B GLY* 3.6 16.6 - - - -
313B ILE 4.3 7.2 - - - -
314B ALA* 4.6 0.2 - - - -
319B LEU 3.5 16.8 - - - -
320B ALA* 2.6 17.6 + - - +
322B VAL* 1.3 67.6 - - - +
324B SER* 1.3 57.5 + - - +
325B ASP 3.0 2.2 - - - -
326B LYS* 2.5 37.6 + - - +
327B ASN 3.9 1.9 + - - -
333B TYR* 3.6 20.9 + - + +
335B ILE* 3.5 35.2 - - - -
345B PHE* 4.1 9.2 - - - -
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Residues in contact with SER 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B HIS* 3.1 41.4 + - - -
107B ASP* 5.0 4.3 - - - -
310B SER* 3.6 12.2 - - - -
311B ALA* 3.5 19.4 + - - +
312B GLY* 3.7 2.1 - - - -
320B ALA 3.2 4.1 + - - -
321B LYS 2.6 16.0 + - - -
323B CYS* 1.3 79.2 - - - +
325B ASP* 1.3 79.0 + - - +
326B LYS 3.6 0.7 + - - -
327B ASN 4.3 1.4 - - - -
328B LYS* 3.4 19.9 + - - +
331B GLY 4.8 0.9 - - - +
332B GLN* 5.4 0.2 - - - -
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Residues in contact with ASP 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321B LYS 3.6 4.3 - - - +
322B VAL* 3.5 9.7 + - - +
323B CYS 3.0 1.0 - - - -
324B SER* 1.3 102.3 + - - +
326B LYS* 1.3 65.0 + - - +
327B ASN 3.5 0.7 - - - -
328B LYS* 3.5 26.6 - - + +
353B LYS* 5.3 6.2 + - - -
1521B DTP 3.5 22.7 + - - -
1522B CA 2.9 22.4 - - - -
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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