Contacts of the helix formed by residues 677 - 684 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A TRP* 2.9 33.7 + - + +
217A MET* 4.0 25.3 - - + +
218A TRP 5.0 0.6 - - - +
333A LYS* 3.6 40.6 - - + -
336A ASP* 4.0 11.4 - - + -
337A GLY* 3.4 37.5 - - - +
340A GLU* 3.1 42.7 + - + +
589A TYR* 4.5 0.6 + - - +
676A ASN* 1.3 76.3 - - - +
678A GLU* 1.3 80.0 + - + +
679A SER 3.3 1.2 + - - -
680A VAL* 3.4 23.1 - - + +
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Residues in contact with GLU 678 (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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341A GLY* 5.7 2.0 - - - -
344A ARG* 2.7 47.5 + - - +
589A TYR* 2.6 32.9 + - - -
591A PRO* 3.7 21.3 - - - +
597A TYR* 5.0 1.7 + - - -
676A ASN* 3.3 3.8 + - - +
677A TRP* 1.3 94.8 + - + +
679A SER* 1.3 60.2 + - - +
680A VAL 3.3 0.8 + - - -
681A SER* 3.6 5.6 + - - -
682A SER* 5.2 0.7 + - - -
687A ASP* 5.6 1.9 - - - +
690A MET* 3.7 29.8 - - + +
691A THR* 5.0 0.9 + - - -
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Residues in contact with SER 679 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675A GLY* 3.6 2.1 - - - -
676A ASN* 2.8 42.9 + - - +
678A GLU* 1.3 76.9 - - - +
680A VAL* 1.3 66.8 + - - +
681A SER 3.3 0.9 - - - -
682A SER* 3.0 24.8 + - - -
690A MET 3.5 11.7 + - - -
691A THR* 3.9 19.4 - - - +
692A ARG 4.0 4.3 - - - -
2C TYR* 3.4 20.2 + - - -
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Residues in contact with VAL 680 (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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216A TRP* 3.4 39.0 - - + -
334A ASN* 3.6 20.9 - - - +
337A GLY* 3.3 13.2 - - - +
338A GLN* 3.3 46.1 - - + +
676A ASN 4.1 4.9 - - - +
677A TRP* 3.4 12.1 - - + +
678A GLU 3.3 0.8 - - - -
679A SER* 1.3 86.4 - - - +
681A SER* 1.3 58.5 + - - +
682A SER 3.0 5.4 + - - -
683A ASN* 3.2 13.5 + - - +
2C TYR* 4.5 6.3 - - + +
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Residues in contact with SER 681 (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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338A GLN* 3.9 5.2 - - - -
341A GLY* 3.5 30.6 + - - -
342A PHE* 3.7 30.8 - - - -
344A ARG* 3.6 13.2 + - - -
345A ILE* 4.5 9.7 - - - +
678A GLU 3.6 3.0 + - - -
680A VAL* 1.3 78.0 - - - +
682A SER* 1.3 55.8 + - - +
683A ASN* 3.0 6.3 - - - -
684A TRP* 3.0 11.0 + - - +
685A VAL* 3.0 24.5 + - - +
687A ASP* 5.8 1.9 - - - +
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Residues in contact with SER 682 (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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278A ARG* 2.8 35.0 + - - +
678A GLU 5.2 0.5 + - - -
679A SER 3.0 14.5 + - - -
680A VAL 3.0 1.4 + - - -
681A SER* 1.3 74.7 + - - +
683A ASN* 1.3 62.8 + - - +
684A TRP 3.1 1.1 + - - -
685A VAL 3.4 13.4 + - - -
686A PHE* 4.0 15.0 - - - -
687A ASP* 3.2 17.2 + - - +
691A THR* 2.6 31.6 + - - -
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Residues in contact with ASN 683 (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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275A SER* 3.2 10.0 + - - +
276A THR* 3.2 30.0 - - - +
277A ASN* 2.8 50.3 + - - +
278A ARG* 3.4 7.2 + - - +
293A TYR* 3.5 10.1 + - - -
338A GLN* 3.7 11.6 + - - +
653A THR* 4.7 7.6 + - - +
679A SER 4.7 0.2 + - - -
680A VAL 3.2 13.9 + - - +
681A SER 3.0 0.2 - - - -
682A SER* 1.3 78.6 - - - +
684A TRP* 1.3 83.9 + - - +
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Residues in contact with TRP 684 (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 ASN* 3.6 40.5 - - + +
278A ARG* 3.8 20.8 - - - +
280A ALA* 3.6 25.4 - - + -
284A GLU* 3.9 8.1 - - + -
285A PHE* 3.6 42.6 - + + -
288A THR* 3.3 36.1 - - + -
293A TYR* 2.9 24.6 + - - -
338A GLN* 3.2 24.6 - - - +
342A PHE* 3.5 17.5 - + + -
351A LYS* 4.6 9.4 + - + +
681A SER 3.0 4.9 + - - +
682A SER 4.1 0.9 - - - -
683A ASN* 1.3 91.1 - - - +
685A VAL* 1.3 67.1 + - + +
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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