Contacts of the helix formed by residues 358 - 370 (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 ASP 358 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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292A GLY* 5.5 2.2 - - - -
354A TYR* 5.5 0.9 - - - -
356A LYS* 4.0 22.0 - - + +
357A HIS* 1.3 77.3 - - - +
359A PHE* 1.3 71.9 + - + +
360A ALA* 3.2 14.2 + - - +
361A SER* 2.8 39.1 + - - -
362A VAL* 3.1 8.1 + - - +
1074A ARG 5.4 3.4 - - - +
1076A PRO* 3.9 15.7 - - - -
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Residues in contact with PHE 359 (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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358A ASP* 1.3 76.7 - - + +
360A ALA* 1.3 65.8 + - - +
362A VAL* 3.2 9.4 - - + +
363A ARG* 3.0 27.0 + - - +
1073A LEU 3.2 27.4 - - - -
1074A ARG* 3.6 21.1 - - - -
1075A LEU 3.5 19.3 - - - -
1076A PRO* 3.6 16.3 - - + +
1078A CYS 6.0 0.4 - - - -
1081A ILE 4.4 5.6 - - - -
1082A ASP* 3.6 30.1 - - + +
1083A PRO* 3.5 21.5 - - + -
1089A PHE* 3.8 20.0 - + - -
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Residues in contact with ALA 360 (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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354A TYR* 4.2 12.9 + - + -
358A ASP* 3.2 13.5 + - - +
359A PHE* 1.3 79.7 - - - +
361A SER* 1.3 56.6 + - - +
363A ARG* 3.6 8.4 + - - +
364A TYR* 3.1 25.3 + - - +
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Residues in contact with SER 361 (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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285A MET* 4.1 7.6 - - - -
286A TYR* 2.9 25.7 + - - -
354A TYR* 3.7 25.3 - - - -
356A LYS 3.4 15.5 + - - -
357A HIS* 4.3 0.3 + - - -
358A ASP* 2.8 39.1 + - - -
360A ALA* 1.3 69.8 - - - +
362A VAL* 1.3 62.7 + - - -
364A TYR* 3.1 6.1 + - - +
365A ILE* 3.1 26.2 + - - +
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Residues in contact with VAL 362 (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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286A TYR* 4.2 3.6 - - - +
357A HIS* 3.7 32.1 - - + +
358A ASP 3.5 8.1 - - - +
359A PHE* 3.2 22.4 - - + +
361A SER* 1.3 74.7 + - - +
363A ARG* 1.3 58.2 + - + +
365A ILE* 3.2 10.5 + - + +
366A ARG 2.8 25.3 + - - -
787A ILE* 4.3 4.7 - - + -
790A CYS* 3.7 20.9 - - + -
792A ILE* 3.8 10.9 - - + +
1076A PRO* 4.2 4.9 - - + -
1079A ALA* 3.4 32.7 - - + +
1080A GLY 5.1 0.4 - - - +
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Residues in contact with ARG 363 (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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243A ALA 3.6 6.3 + - - -
244A GLY* 4.9 6.6 + - - -
359A PHE 3.0 18.0 + - - +
360A ALA* 3.7 7.4 - - - +
362A VAL* 1.3 78.3 - - - +
364A TYR* 1.3 53.3 + - - +
366A ARG* 3.4 25.1 - - - +
367A ASP* 2.7 55.5 + - - +
834A GLN* 3.1 27.9 + - - +
1079A ALA* 4.4 4.7 - - - -
1080A GLY* 3.0 27.6 + - - +
1082A ASP* 2.7 44.4 + - - +
1084A LEU* 3.9 21.1 - - - +
1085A ASN* 4.5 0.4 - - - +
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Residues in contact with TYR 364 (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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249A LEU* 3.8 25.5 - - + +
281A THR* 3.6 24.9 - - + +
285A MET* 4.1 9.6 - - - -
347A LEU* 3.4 16.1 + - - +
350A ARG* 3.6 24.5 - - - +
351A THR* 2.9 34.4 + - - -
354A TYR* 3.6 46.4 - + + +
360A ALA 3.1 13.9 + - - +
361A SER 3.1 12.3 + - - +
363A ARG* 1.3 76.8 - - - +
365A ILE* 1.3 65.4 + - - +
367A ASP* 3.6 6.1 - - - +
368A ALA* 3.0 23.6 + - - +
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Residues in contact with ILE 365 (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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281A THR* 4.1 6.2 + - - +
282A LEU* 3.7 31.9 - - + +
285A MET* 3.5 43.7 - - + -
286A TYR* 4.6 2.2 - - - +
361A SER 3.1 13.7 + - - +
362A VAL* 3.4 12.1 - - - +
364A TYR* 1.3 77.6 - - + +
366A ARG* 1.3 66.7 + - - +
368A ALA* 3.2 4.1 + - - +
369A MET* 2.8 27.3 + - - +
787A ILE* 4.1 26.5 - - + -
792A ILE* 3.7 19.1 - - + -
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Residues in contact with ARG 366 (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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243A ALA* 3.2 42.6 + - - +
245A LEU* 4.5 0.2 - - - -
362A VAL 2.8 19.3 + - - +
363A ARG* 3.4 21.8 - - - +
365A ILE* 1.3 73.9 - - - +
367A ASP* 1.3 93.0 + - - +
369A MET* 3.1 4.8 + - - +
370A ALA* 3.0 19.9 + - - +
792A ILE* 3.9 13.0 - - + +
793A PRO* 3.8 18.9 - - + +
795A LEU* 4.0 23.6 - - + +
831A ASP 4.8 1.8 + - - -
832A GLY 3.4 24.7 + - - -
833A LEU* 4.2 4.8 - - - +
834A GLN* 4.4 1.8 - - - +
1079A ALA* 3.8 23.9 + - + +
1080A GLY* 3.9 16.1 - - - -
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Residues in contact with ASP 367 (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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244A GLY 4.0 3.3 - - - +
245A LEU* 3.2 22.3 - - + +
246A ASP* 2.9 29.9 + - + +
249A LEU* 3.9 13.5 - - + -
363A ARG* 2.7 33.0 + - - +
364A TYR* 3.6 6.1 - - - +
366A ARG* 1.3 101.7 + - - +
368A ALA* 1.3 63.9 + - - +
370A ALA* 2.9 17.5 + - - +
371A CYS* 3.3 13.2 - - - -
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Residues in contact with ALA 368 (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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249A LEU* 3.8 18.6 - - + +
277A PHE* 3.4 30.2 - - + -
281A THR* 3.6 31.4 - - + +
364A TYR* 3.0 18.3 + - + +
365A ILE 3.5 3.8 - - - +
367A ASP* 1.3 74.7 - - - +
369A MET* 1.3 58.6 + - - +
371A CYS* 3.1 22.9 + - - +
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Residues in contact with MET 369 (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 PHE* 4.4 1.1 - - - -
278A PRO* 3.8 33.2 - - + -
281A THR* 4.6 2.2 - - - +
282A LEU* 3.8 31.9 - - + -
365A ILE* 2.8 25.1 + - - +
366A ARG* 3.1 6.2 + - - +
368A ALA* 1.3 75.7 - - - +
370A ALA* 1.3 57.5 + - - +
371A CYS 3.2 0.4 - - - -
372A THR* 3.7 8.8 + - - +
785A TYR* 3.8 42.6 - - + -
792A ILE* 4.4 7.9 - - + -
793A PRO 5.2 0.2 - - - +
794A ASN* 3.3 29.2 - - + +
795A LEU 5.0 1.1 - - - -
796A SER* 3.2 22.9 + - - -
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Residues in contact with ALA 370 (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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236A LEU* 3.8 11.6 - - - +
239A LEU* 3.9 10.6 - - + +
245A LEU* 3.7 23.6 - - + -
366A ARG 3.0 9.6 + - - +
367A ASP 2.9 13.7 + - - +
369A MET* 1.3 77.0 - - - +
371A CYS* 1.3 62.2 + - - +
372A THR 3.4 5.5 + - - +
795A LEU* 3.5 33.4 - - + -
796A SER* 4.0 6.8 - - - +
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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