Contacts of the helix formed by residues 265 - 274 (chain A) in PDB entry 1MWH
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 265 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A ARG* 4.5 1.2 + - - -
91A ASP* 4.3 12.6 - - - -
93A TYR* 4.0 8.1 - - - +
94A VAL 2.8 21.9 + - - -
95A PRO* 4.3 2.5 - - - -
96A ASN* 3.0 7.1 - - - +
263A SER* 3.1 12.9 + - - -
264A SER* 1.3 84.9 + - - +
266A TYR* 1.3 58.4 + - - +
267A SER 4.2 0.2 + - - -
268A TRP* 3.4 28.2 + - - +
269A PHE* 2.9 26.7 + - - +
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Residues in contact with TYR 266 (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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94A VAL 4.5 1.0 + - - -
96A ASN* 2.9 15.2 + - - +
143A GLN* 4.9 5.8 - - - +
225A ALA* 4.3 15.3 - - + -
228A PRO* 3.6 25.6 - - + -
229A LEU* 3.5 25.6 - - + -
232A ASP* 2.5 32.2 + - - -
257A CYS* 3.4 27.7 - - + +
260A ALA* 3.3 34.5 - - + +
261A ALA* 3.3 16.8 - - + -
265A SER* 1.3 71.3 + - - +
267A SER* 1.3 65.3 + - - +
269A PHE* 3.3 1.9 + - - +
270A ILE* 3.0 40.2 + - + +
375A ILE* 3.8 13.9 - - + -
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Residues in contact with SER 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A TYR* 3.4 25.5 - - - -
94A VAL 5.0 1.5 + - - -
143A GLN* 4.1 17.2 + - - -
265A SER* 3.5 1.2 + - - -
266A TYR* 1.3 79.3 - - - +
268A TRP* 1.3 63.4 + - - +
270A ILE* 3.3 2.4 + - - +
271A LEU* 3.0 23.0 + - - +
375A ILE* 4.1 14.8 - - - -
377A LEU* 3.2 35.5 - - - +
378A VAL 4.7 5.8 - - - -
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Residues in contact with TRP 268 (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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87A GLN* 3.2 56.2 + - + -
90A ASP* 3.6 16.3 - - + +
91A ASP* 3.6 37.0 - - - +
93A TYR* 4.3 14.7 - + + +
263A SER* 5.0 5.2 - - - -
264A SER* 5.0 1.3 - - - -
265A SER* 3.4 29.7 + - - +
266A TYR 3.3 0.2 - - - -
267A SER* 1.3 78.4 - - - +
269A PHE* 1.3 90.7 + + + +
271A LEU* 3.1 7.1 + - + +
272A LYS* 3.0 56.5 + - + +
338A TYR* 3.7 26.5 - + - -
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Residues in contact with PHE 269 (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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256A ILE* 4.0 4.9 - - + -
259A HIS* 3.9 27.1 - + + -
260A ALA* 3.5 22.0 - - + -
263A SER* 3.6 24.2 - - - +
265A SER 2.9 21.1 + - - +
266A TYR 3.7 3.8 - - - +
268A TRP* 1.3 92.2 - + + +
270A ILE* 1.3 61.5 + - + +
272A LYS* 3.4 2.8 + - - -
273A THR* 2.9 37.5 + - - +
338A TYR* 3.4 44.0 - + + -
340A LEU* 3.7 23.6 - - + -
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Residues in contact with ILE 270 (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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256A ILE* 4.6 18.2 - - + -
257A CYS* 4.9 2.5 - - - -
260A ALA* 3.8 18.2 - - + -
266A TYR* 3.0 44.2 + - + +
267A SER* 3.6 5.8 - - - +
269A PHE* 1.3 73.4 - - + +
271A LEU* 1.3 61.2 + - - +
273A THR* 3.7 3.1 - - - +
274A LYS* 2.9 36.6 + - + +
372A THR* 5.6 0.7 - - + -
373A SER* 3.5 40.2 - - - +
375A ILE* 4.5 9.2 - - + -
377A LEU* 5.1 7.6 - - + -
522A GLN* 5.1 5.4 - - + -
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Residues in contact with LEU 271 (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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90A ASP* 4.6 21.8 - - + +
93A TYR* 3.7 35.4 - - + +
267A SER 3.0 13.7 + - - +
268A TRP* 3.3 9.9 - - + +
270A ILE* 1.3 80.2 - - - +
272A LYS* 1.3 66.3 + - - +
273A THR 3.5 0.2 + - - -
274A LYS* 3.6 47.8 - - - +
377A LEU* 3.8 18.8 - - + +
522A GLN 4.4 2.0 - - - +
523A ARG* 4.4 2.2 - - - -
524A ARG* 4.4 17.9 - - + +
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Residues in contact with LYS 272 (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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90A ASP* 2.6 33.7 + - - +
268A TRP* 3.0 52.6 + - + +
269A PHE 3.9 4.3 - - - +
270A ILE 3.3 0.2 - - - -
271A LEU* 1.3 83.5 - - + +
273A THR* 1.3 60.0 + - + +
274A LYS 3.7 0.2 - - - -
275A SER* 5.3 1.1 + - - -
334A LEU* 3.5 23.9 - - - +
338A TYR* 3.4 35.8 + - + +
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Residues in contact with THR 273 (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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256A ILE* 4.1 11.8 - - - +
269A PHE* 2.9 37.6 + - + +
270A ILE* 3.9 4.9 + - - +
272A LYS* 1.3 80.8 - - - +
274A LYS* 1.3 59.4 + - - +
275A SER 3.1 6.3 - - - -
276A ILE* 2.8 42.5 - - + +
334A LEU* 4.4 4.0 - - + -
338A TYR* 3.6 38.6 - - + -
340A LEU* 4.0 6.5 - - + -
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Residues in contact with LYS 274 (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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270A ILE* 2.9 15.9 + - + +
271A LEU* 3.6 34.3 - - - +
272A LYS 3.7 0.8 - - - -
273A THR* 1.3 76.1 - - - +
275A SER* 1.3 65.4 + - - +
276A ILE* 3.3 0.4 - - - -
277A PHE 4.7 0.5 + - - -
278A PRO* 3.7 13.5 - - - +
372A THR* 3.7 21.7 - - + +
522A GLN* 3.2 53.2 + - + +
523A ARG* 4.8 5.5 - - - +
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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