Contacts of the helix formed by residues 733 - 745 (chain B) in PDB entry 4MS0
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 VAL 733 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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774A TRP* 4.5 11.2 - - + -
775A ILE 4.8 1.1 - - - +
635B LEU* 4.1 20.9 - - + -
638B TYR* 3.0 33.4 + - + -
639B PHE* 4.2 16.2 - - + -
675B LEU* 3.9 23.1 - - + -
729B PHE* 2.8 41.2 + - + +
731B ASN 3.5 0.2 - - - -
732B ALA* 1.3 90.8 - - + +
734B ALA* 1.3 65.5 + - - +
735B ILE 3.5 1.3 - - - -
736B PRO* 3.4 2.4 - - - +
737B CYS* 3.2 6.9 + - - +
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Residues in contact with ALA 734 (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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675B LEU* 4.7 4.9 - - + -
678B VAL* 3.9 19.1 - - + -
729B PHE* 3.1 15.2 + - + +
730B TYR* 3.9 15.3 - - + -
733B VAL* 1.3 78.1 - - - +
735B ILE* 1.3 66.9 + - - +
737B CYS* 3.1 6.1 + - - +
738B TYR* 3.0 34.3 + - + -
755B CYS* 3.7 20.4 - - - -
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Residues in contact with ILE 735 (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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480A GLY 5.0 1.1 - - - +
481A PRO* 3.9 29.4 - - + +
730B TYR 2.8 23.2 + - - +
731B ASN* 4.6 4.0 - - - +
734B ALA* 1.3 71.2 - - - +
736B PRO* 1.3 63.8 - - + +
738B TYR 3.8 0.3 - - - -
739B THR* 2.6 46.8 + - - +
752B LEU* 4.1 7.3 - - + +
755B CYS* 3.6 22.9 - - - -
756B ARG* 3.8 29.2 - - + +
759B LEU* 3.7 27.6 - - + -
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Residues in contact with PRO 736 (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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638B TYR* 3.6 11.0 - - - +
642B ARG* 3.5 21.9 - - - +
731B ASN 3.5 20.9 - - - +
732B ALA 3.9 11.2 - - - +
733B VAL 3.4 10.1 - - - +
735B ILE* 1.3 97.0 - - + +
737B CYS* 1.3 56.4 + - - +
739B THR* 3.7 5.5 - - - -
740B THR* 2.9 37.6 + - - +
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Residues in contact with CYS 737 (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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638B TYR* 3.1 24.8 + - + +
642B ARG* 4.5 0.7 - - - +
668B LEU* 3.9 19.0 - - - +
671B THR* 4.0 11.7 - - + -
672B ALA* 3.6 41.1 - - - -
675B LEU* 4.9 3.8 - - + -
733B VAL 3.2 6.0 + - - +
734B ALA* 3.1 12.4 + - - +
736B PRO* 1.3 79.5 - - - +
738B TYR* 1.3 63.1 + - + +
740B THR* 3.8 2.3 - - - -
741B LEU* 2.9 28.4 + - - +
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Residues in contact with TYR 738 (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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672B ALA* 2.7 52.2 + - + -
675B LEU* 3.3 25.1 + - + +
676B CYS* 3.4 5.5 - - - -
678B VAL* 3.7 22.2 - - + -
679B THR* 3.5 14.5 - - + +
734B ALA* 3.0 30.5 + - + +
737B CYS* 1.3 74.9 - - - +
739B THR* 1.3 59.1 + - - +
741B LEU* 3.9 5.5 - - + +
742B THR* 2.8 35.7 + - - -
751B LEU* 3.6 28.0 - - + -
752B LEU* 3.8 26.2 - - + +
755B CYS* 4.0 15.5 - - + -
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Residues in contact with THR 739 (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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481A PRO 5.1 0.3 + - - -
483A GLU* 6.0 7.4 - - + +
484A ASN* 6.3 0.7 - - + +
735B ILE* 2.6 35.7 + - - +
736B PRO* 3.7 6.3 - - - -
738B TYR* 1.3 78.4 - - - +
740B THR* 1.3 63.3 + - - +
742B THR* 3.5 2.6 + - - -
743B GLN* 3.2 41.2 + - + +
752B LEU* 3.4 25.1 - - + +
756B ARG* 4.8 6.6 + - - +
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Residues in contact with THR 740 (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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642B ARG* 3.2 36.2 + - + -
645B LEU* 4.1 11.2 - - + -
646B GLU* 4.2 14.2 - - - +
649B TYR* 6.2 0.9 - - + -
668B LEU* 3.8 15.3 - - + -
736B PRO 2.9 16.6 + - - -
737B CYS 3.9 1.8 - - - -
739B THR* 1.3 75.2 - - - +
741B LEU* 1.3 65.2 + - - +
743B GLN* 3.2 15.6 + - - +
744B ILE* 3.1 34.0 + - + +
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Residues in contact with LEU 741 (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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540B ILE* 4.2 6.1 - - + -
665B VAL* 5.0 2.9 - - + +
668B LEU* 3.6 16.6 - - + +
669B MET* 3.8 38.4 - - + +
672B ALA* 3.7 23.6 - - + -
737B CYS 2.9 18.9 + - - +
738B TYR* 3.9 8.7 - - + +
740B THR* 1.3 75.5 - - - +
742B THR* 1.3 51.6 + - - +
744B ILE* 3.2 4.3 + - + +
745B LEU* 2.7 46.8 + - + +
748B THR* 3.6 21.3 - - + +
751B LEU* 3.8 20.4 - - + -
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Residues in contact with THR 742 (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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738B TYR 2.8 23.1 + - - -
739B THR 3.7 4.5 - - - -
741B LEU* 1.3 71.0 - - - +
743B GLN* 1.3 67.4 + - + +
745B LEU 3.7 0.7 - - - -
746B PRO* 3.1 26.3 - - + +
748B THR* 3.6 11.9 + - - -
749B GLU* 3.5 44.0 + - + +
752B LEU* 3.7 20.4 + - + +
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Residues in contact with GLN 743 (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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484A ASN* 5.7 7.3 - - - +
646B GLU* 5.0 9.0 - - - +
649B TYR* 3.4 58.6 + - + +
650B GLN* 4.8 8.0 + - - +
739B THR* 3.2 31.7 + - + +
740B THR* 3.2 19.0 + - + +
742B THR* 1.3 80.0 - - + +
744B ILE* 1.3 62.4 + - + +
746B PRO* 4.2 9.1 - - - +
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Residues in contact with ILE 744 (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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645B LEU* 3.8 43.1 - - + +
649B TYR* 4.6 13.7 - - + -
654B LEU* 3.9 27.6 - - + -
656B LEU* 5.2 5.6 - - + +
665B VAL* 3.9 22.4 - - + -
668B LEU* 4.4 8.7 - - + -
740B THR* 3.1 23.4 + - + +
741B LEU* 4.0 3.6 - - + +
743B GLN* 1.3 79.1 - - + +
745B LEU* 1.3 77.4 + - + +
746B PRO* 3.5 6.3 - - - +
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Residues in contact with LEU 745 (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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540B ILE* 4.0 26.2 - - + -
544B ASN* 3.7 23.6 - - + +
547B LEU* 5.4 5.2 - - + -
548B PHE* 4.6 10.3 - - + -
656B LEU* 5.3 11.0 - - + -
665B VAL* 4.6 8.5 - - + -
669B MET* 4.1 15.5 - - - -
741B LEU* 2.7 32.6 + - + +
742B THR 3.3 4.1 - - - +
744B ILE* 1.3 93.8 - - + +
746B PRO* 1.4 64.5 - - - +
747B PRO* 3.3 2.9 - - - -
748B THR* 2.8 30.4 + - + -
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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