Contacts of the helix formed by residues 677 - 684 (chain B) in PDB entry 3WOO
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 TRP 677 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B TRP* 2.8 34.3 + + + +
217B MET* 4.0 25.3 - - + +
218B TRP 5.0 0.4 - - - +
333B LYS* 3.7 41.3 - - + -
336B ASP* 4.0 10.5 - - + -
337B GLY* 3.4 34.1 + - - +
340B GLU* 3.0 42.2 + - + +
589B TYR* 4.5 0.8 + - - +
676B ASN* 1.3 73.6 - - - +
678B GLU* 1.3 81.7 + - + +
679B SER 3.3 1.0 + - - -
680B VAL* 3.4 22.7 - - + +
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Residues in contact with GLU 678 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B GLY* 5.7 4.5 - - - -
344B ARG* 3.2 37.7 + - - +
589B TYR* 2.7 34.0 + - - -
591B PRO* 3.8 19.6 - - + +
597B TYR* 5.0 2.3 + - - -
676B ASN* 3.1 4.5 + - - +
677B TRP* 1.3 93.0 + - + +
679B SER* 1.3 61.3 + - - +
680B VAL 3.4 0.9 - - - -
681B SER* 3.7 8.1 + - - -
682B SER* 5.0 1.2 + - - -
690B MET* 3.7 35.1 - - + +
691B THR* 5.0 0.7 + - - -
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Residues in contact with SER 679 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675B GLY* 3.6 2.1 - - - -
676B ASN* 2.7 43.3 + - - +
678B GLU* 1.3 79.7 - - - +
680B VAL* 1.3 65.2 + - - +
681B SER 3.3 0.7 - - - -
682B SER* 3.1 24.2 + - - -
690B MET 3.4 11.5 + - - -
691B THR* 3.9 19.4 - - - +
692B ARG 4.0 4.5 - - - -
2D TYR* 3.4 19.3 + - - -
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Residues in contact with VAL 680 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B TRP* 3.5 43.3 - - + -
334B ASN* 3.6 18.8 - - - +
337B GLY* 3.3 12.1 - - - +
338B GLN* 3.3 38.2 + - + +
676B ASN 4.2 4.9 - - - +
677B TRP* 3.4 12.8 - - + +
678B GLU 3.4 0.6 - - - -
679B SER* 1.3 79.7 - - - +
681B SER* 1.3 62.2 + - - +
682B SER 3.0 6.1 + - - -
683B ASN* 3.1 20.4 + - - +
2D TYR* 4.4 6.5 - - + +
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Residues in contact with SER 681 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B GLN* 3.9 8.3 - - - +
341B GLY* 3.6 28.2 + - - -
342B PHE* 3.7 31.7 - - - -
344B ARG* 4.1 6.6 + - - -
345B ILE* 4.7 6.4 - - - +
678B GLU 3.7 12.5 + - - -
680B VAL* 1.3 75.3 - - - +
682B SER* 1.3 55.7 + - - +
683B ASN 3.0 5.8 - - - -
684B TRP* 3.0 21.4 + - - +
685B VAL* 3.1 13.7 + - - +
687B ASP* 6.0 0.3 - - - +
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Residues in contact with SER 682 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B ARG* 2.9 35.0 + - - +
678B GLU 5.0 1.2 + - - -
679B SER* 3.1 13.8 + - - -
680B VAL 3.0 1.4 + - - -
681B SER* 1.3 73.6 + - - +
683B ASN* 1.3 61.3 + - - +
684B TRP 3.0 2.4 + - - -
685B VAL 3.2 12.1 + - - -
686B PHE* 3.8 18.3 + - - -
687B ASP* 3.1 16.3 + - - +
691B THR* 2.6 31.0 + - - -
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Residues in contact with ASN 683 (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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275B SER* 3.4 8.7 - - - +
276B THR* 3.2 32.5 - - + +
277B ASN* 2.8 49.3 + - - +
278B ARG* 3.4 6.0 + - - +
293B TYR* 3.4 9.5 + - - -
338B GLN* 3.5 12.5 + - - +
653B THR* 4.9 6.0 + - - +
679B SER 4.7 0.2 + - - -
680B VAL 3.1 15.5 + - - +
682B SER* 1.3 78.6 - - - +
684B TRP* 1.4 83.9 + - - +
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Residues in contact with TRP 684 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B ASN* 3.3 43.4 - - + +
278B ARG* 3.7 21.2 - - - +
280B ALA* 3.5 26.7 - - + -
284B GLU* 4.1 8.1 - - + -
285B PHE* 3.8 35.2 - + + -
288B THR* 3.4 38.1 - - + -
293B TYR* 2.9 17.4 + - - -
338B GLN* 3.1 18.4 - - - -
342B PHE* 3.4 20.8 - + + -
351B LYS* 4.8 9.2 + - + +
681B SER 3.0 5.4 + - - +
682B SER 4.2 0.9 - - - -
683B ASN* 1.4 104.9 - - - +
685B VAL* 1.3 67.0 + - + +
686B PHE 4.2 0.2 - - - -
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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