Contacts of the helix formed by residues 444 - 454 (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 444 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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440A PRO 3.5 2.1 + - - +
441A ARG* 2.9 26.3 + - + +
443A TRP* 1.3 78.5 - - - +
445A PRO* 1.3 70.7 - - - +
446A LEU* 2.7 35.9 + - - +
447A PHE* 3.0 18.3 + - + +
448A GLN* 3.1 12.6 + - - +
987A ARG* 2.9 25.9 + - - +
1150A LEU* 5.9 0.3 - - - -
1151A GLN* 5.0 1.4 + - - +
1154A GLU* 3.4 21.7 - - - +
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Residues in contact with PRO 445 (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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443A TRP 3.6 8.0 - - - +
444A ASP* 1.3 90.1 - - - +
446A LEU* 1.3 55.5 + - - +
448A GLN* 3.3 11.5 + - + +
449A ALA* 2.9 27.4 + - - +
981A ASN* 4.0 30.3 - - + +
983A GLU* 3.6 34.5 - - + +
984A LEU* 4.1 20.5 - - + +
987A ARG* 3.8 13.5 - - - +
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Residues in contact with LEU 446 (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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444A ASP* 2.7 20.9 + - - +
445A PRO* 1.3 71.5 - - - +
447A PHE* 1.3 65.8 + - - +
449A ALA* 3.0 3.1 + - + +
450A ILE* 2.9 50.1 + - + +
984A LEU* 4.1 10.9 - - + +
987A ARG* 3.9 1.4 - - - +
1009A LEU* 4.5 1.6 - - + -
1112A MET* 4.9 6.1 - - + -
1115A THR* 5.5 0.9 - - - +
1116A VAL* 4.5 14.1 - - + +
1148A VAL 3.5 18.8 - - - +
1149A GLY* 3.5 34.5 - - - +
1150A LEU* 3.8 22.2 - - + -
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Residues in contact with PHE 447 (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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436A MET* 5.2 0.7 - - + -
441A ARG* 3.2 61.7 - - + +
442A THR* 3.5 34.3 - - + -
444A ASP* 3.0 9.8 + - + +
446A LEU* 1.3 79.9 - - - +
448A GLN* 1.3 58.6 + - + +
450A ILE* 3.2 14.5 + - + +
451A MET* 3.0 37.3 + - + +
544A LEU* 3.5 34.3 - - + -
619A PHE* 4.7 2.5 - + - -
1114A LYS* 3.7 24.5 - - - -
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Residues in contact with GLN 448 (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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442A THR 3.3 13.6 - - - +
443A TRP* 3.9 17.4 - - - +
444A ASP 3.1 8.9 + - - +
445A PRO* 3.7 11.2 - - + +
447A PHE* 1.3 75.2 - - + +
449A ALA* 1.3 65.2 + - - +
451A MET* 3.8 4.7 - - - +
452A ARG* 3.0 30.4 + - - +
618A PRO 4.7 2.8 + - - +
619A PHE* 3.2 42.4 - - + +
620A MET* 3.0 34.3 - - + +
621A GLY 4.8 0.4 - - - +
981A ASN* 5.4 6.9 - - - +
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Residues in contact with ALA 449 (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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445A PRO 2.9 13.4 + - - +
446A LEU* 3.0 8.7 + - + +
448A GLN* 1.3 75.8 - - - +
450A ILE* 1.3 60.0 + - - +
452A ARG* 3.0 12.9 + - - +
453A SER* 2.9 31.1 + - - -
978A LEU* 4.2 23.5 - - + +
984A LEU* 3.6 25.4 - - + -
1116A VAL* 4.5 7.2 - - + -
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Residues in contact with ILE 450 (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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441A ARG* 5.0 12.6 - - - +
446A LEU* 2.9 42.9 + - + +
447A PHE* 3.4 14.8 - - + +
449A ALA* 1.3 76.7 - - - +
451A MET* 1.3 59.9 + - + +
453A SER* 3.0 10.1 + - - +
454A GLN* 3.0 28.2 + - + +
1114A LYS* 4.5 26.5 - - + +
1115A THR* 3.6 44.4 - - - +
1116A VAL* 3.8 5.8 - - + +
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Residues in contact with MET 451 (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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447A PHE* 3.0 43.6 + - + +
448A GLN* 3.9 2.7 - - - +
449A ALA 3.2 0.2 - - - -
450A ILE* 1.3 79.1 - - + +
452A ARG* 1.3 59.5 + - - +
453A SER 3.5 0.5 + - - -
454A GLN* 3.6 32.5 + - - +
455A TYR* 3.2 22.8 - - + -
540A ALA* 4.5 17.7 - - + +
543A THR* 4.8 11.0 - - + -
544A LEU* 3.7 32.5 - - + -
547A ASP* 5.6 1.8 - - - +
620A MET* 3.4 25.6 - - + +
685A THR* 5.9 0.4 - - - +
1114A LYS* 5.0 7.4 - - - -
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Residues in contact with ARG 452 (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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448A GLN* 3.0 22.2 + - - +
449A ALA* 3.0 10.5 + - - +
451A MET* 1.3 77.3 - - - +
453A SER* 1.3 57.4 + - - +
455A TYR* 3.6 16.4 - - - +
456A VAL* 3.1 10.6 - - - +
498A ALA 5.8 1.0 + - - -
537A GLN* 3.6 12.3 - - - +
620A MET* 3.1 49.0 + - + +
977A TYR* 2.7 92.0 + - + +
978A LEU* 5.3 2.8 + - + +
980A GLN* 3.5 32.1 + - - +
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Residues in contact with SER 453 (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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449A ALA 2.9 12.9 + - - -
450A ILE* 3.0 13.2 + - - +
452A ARG* 1.3 75.0 - - - +
454A GLN* 1.3 67.7 + - - +
455A TYR 3.1 3.1 - - - -
456A VAL* 2.9 21.6 + - - +
978A LEU* 4.5 2.7 - - - -
1016A TRP* 3.7 23.1 - - - -
1116A VAL* 3.7 9.1 - - - -
1117A SER* 2.8 39.9 + - - -
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Residues in contact with GLN 454 (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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450A ILE* 3.0 12.8 + - + +
451A MET* 3.7 38.1 - - - +
452A ARG 3.5 0.4 - - - -
453A SER* 1.3 80.0 + - - +
455A TYR* 1.3 58.8 + - + +
456A VAL 3.7 0.5 + - - -
457A THR* 3.8 12.6 - - - +
543A THR* 4.8 5.0 - - - +
685A THR* 3.7 38.3 + - + +
1117A SER* 4.4 8.4 + - - -
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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