Contacts of the helix formed by residues 634 - 651 (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 ASP 634 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572B ASN* 3.6 11.8 - - - +
589B SER* 2.7 31.1 + - - +
592B GLU* 3.6 29.1 - - + +
631B ILE 3.0 15.7 + - - +
632B ALA 3.7 3.6 - - - +
633B THR* 1.3 75.4 + - - +
635B LEU* 1.3 60.6 + - - +
636B ALA* 3.4 21.3 + - - +
637B LEU* 2.8 37.4 + - + +
638B TYR 3.5 2.4 + - - -
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Residues in contact with LEU 635 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
774A TRP* 5.6 5.6 - - + +
632B ALA 5.3 0.2 - - - -
633B THR 3.1 9.0 + - - +
634B ASP* 1.3 72.7 + - - +
636B ALA* 1.3 62.2 + - - +
638B TYR* 3.0 36.5 + - + +
639B PHE* 3.3 32.8 - - + -
671B THR* 3.8 22.4 - - + -
675B LEU* 4.6 9.6 - - + -
729B PHE* 4.7 13.2 - - + -
733B VAL* 4.1 23.3 - - + -
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Residues in contact with ALA 636 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634B ASP* 3.0 19.9 + - - +
635B LEU* 1.3 78.1 - - - +
637B LEU* 1.3 63.6 - - + +
639B PHE* 4.1 17.4 + - - +
640B GLY 4.7 2.3 + - - -
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Residues in contact with LEU 637 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589B SER* 3.8 11.7 - - - +
631B ILE* 3.6 41.7 - - + +
632B ALA* 4.9 7.6 - - - +
634B ASP* 2.8 19.1 + - + +
636B ALA* 1.3 82.1 - - + +
638B TYR* 1.3 62.4 + - - +
639B PHE 3.4 0.4 + - - -
640B GLY* 3.7 2.8 + - - -
641B ASN* 3.2 22.0 + - + +
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Residues in contact with TYR 638 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632B ALA 5.0 2.9 - - - +
634B ASP 3.5 2.6 + - - +
635B LEU* 3.0 34.8 + - + +
637B LEU* 1.3 79.6 - - - +
639B PHE* 1.3 101.3 + + - +
641B ASN* 3.2 8.1 + - + +
642B ARG* 2.8 57.0 + - + -
668B LEU* 3.8 12.1 - - + -
671B THR* 3.7 29.8 - - + +
732B ALA 5.0 0.4 + - - -
733B VAL* 3.0 30.1 + - + -
736B PRO* 3.6 4.7 - - - +
737B CYS* 3.1 32.9 + - + -
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Residues in contact with PHE 639 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
774A TRP* 6.4 0.4 - + - -
775A ILE 4.1 19.3 - - - -
635B LEU* 3.3 41.3 - - + -
636B ALA* 4.1 11.2 - - - +
637B LEU 3.4 0.8 - - - -
638B TYR* 1.3 102.5 - + - +
640B GLY* 1.3 63.4 + - - +
642B ARG* 3.5 5.7 + - - +
643B LYS* 3.0 25.7 + - - +
732B ALA 4.2 13.2 - - - -
733B VAL* 4.2 16.4 - - + -
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Residues in contact with GLY 640 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636B ALA 4.7 2.8 + - - -
637B LEU 3.7 5.2 + - - -
638B TYR 3.4 0.2 - - - -
639B PHE* 1.3 77.2 - - - +
641B ASN* 1.3 57.1 + - - +
643B LYS* 3.3 6.9 + - - +
644B GLN* 2.9 40.7 + - - +
664B ARG* 4.6 0.9 - - - -
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Residues in contact with ASN 641 (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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637B LEU* 3.2 14.0 + - + +
638B TYR* 3.2 13.1 + - - +
640B GLY* 1.3 73.8 - - - +
642B ARG* 1.3 57.7 + - - +
644B GLN* 3.4 2.4 + - - +
645B LEU* 2.9 42.0 + - - +
664B ARG* 2.9 69.7 + - - +
667B GLY* 3.9 6.6 - - - -
668B LEU* 3.5 17.6 - - - +
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Residues in contact with ARG 642 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638B TYR* 2.8 55.9 + - + +
639B PHE* 4.0 4.8 + - - +
641B ASN* 1.3 70.3 - - - +
643B LYS* 1.3 89.5 + - - +
645B LEU* 2.9 11.3 + - - +
646B GLU* 2.8 56.7 + - - +
668B LEU* 4.3 6.7 - - + -
736B PRO* 3.5 24.7 + - - +
740B THR* 3.2 38.3 + - + +
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Residues in contact with LYS 643 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639B PHE 3.0 18.1 + - - +
640B GLY* 3.6 7.0 - - - +
642B ARG* 1.3 95.6 - - - +
644B GLN* 1.3 77.3 + - - +
646B GLU* 3.4 4.5 + - - +
647B GLU* 3.4 39.1 + - + +
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Residues in contact with GLN 644 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640B GLY* 2.9 23.7 + - - +
641B ASN 3.6 0.9 - - - +
643B LYS* 1.3 93.6 - - - +
645B LEU* 1.3 63.2 + - - +
647B GLU* 3.4 25.6 + - - +
648B MET* 3.2 31.3 + - - +
664B ARG* 3.6 39.3 - - - +
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Residues in contact with LEU 645 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641B ASN* 2.9 28.3 + - - +
642B ARG* 2.9 7.2 + - - +
644B GLN* 1.3 73.9 - - - +
646B GLU* 1.3 65.7 + - - +
648B MET* 3.2 8.3 + - + +
649B TYR* 3.0 24.9 + - - +
654B LEU* 3.8 15.8 - - + +
661B HIS 4.7 0.2 - - - +
664B ARG* 3.5 40.8 - - + +
665B VAL* 3.8 26.7 - - + +
668B LEU* 3.8 24.0 - - + -
740B THR* 4.1 6.3 - - + -
744B ILE* 3.8 17.8 - - + +
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Residues in contact with GLU 646 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A GLU* 5.4 7.4 - - - +
642B ARG* 2.8 54.4 + - - +
643B LYS* 3.7 9.4 - - - +
645B LEU* 1.3 72.7 - - - +
647B GLU* 1.3 57.6 + - + +
649B TYR* 3.4 5.3 + - - +
650B GLN* 2.9 43.4 + - + +
740B THR* 4.2 9.5 - - - +
743B GLN* 5.0 10.5 - - - +
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Residues in contact with GLU 647 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643B LYS* 3.4 26.7 + - + +
644B GLN* 3.6 32.4 + - - +
645B LEU 3.3 0.2 - - - -
646B GLU* 1.3 76.4 - - + +
648B MET* 1.3 57.8 + - + +
650B GLN* 3.4 4.6 + - - -
651B THR* 2.6 47.2 + - + +
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Residues in contact with MET 648 (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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644B GLN* 3.2 22.9 + - - +
645B LEU* 3.2 13.4 + - + +
647B GLU* 1.3 79.6 - - + +
649B TYR* 1.3 57.8 + - - +
652B GLY* 3.0 7.4 + - - -
653B SER* 2.9 45.5 + - - +
654B LEU* 3.2 28.4 + - + +
661B HIS* 3.2 52.5 - - + +
664B ARG* 4.4 15.7 - - - -
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Residues in contact with TYR 649 (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 3.0 16.4 + - - +
646B GLU* 3.7 4.3 - - - +
648B MET* 1.3 76.1 - - - +
650B GLN* 1.3 89.8 + - + +
652B GLY* 3.0 14.8 + - - -
654B LEU* 4.1 14.9 - - + +
740B THR* 6.2 1.1 - - + -
743B GLN* 3.4 63.5 + - + +
744B ILE* 4.6 16.2 - - + -
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Residues in contact with GLN 650 (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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646B GLU* 2.9 34.5 + - + +
647B GLU* 3.9 5.2 - - - +
649B TYR* 1.3 102.3 - - + +
651B THR* 1.3 65.0 + - + +
652B GLY 3.5 0.9 + - - -
743B GLN* 4.8 8.5 + - - +
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Residues in contact with THR 651 (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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647B GLU* 2.6 28.6 + - + +
650B GLN* 1.3 80.9 - - + +
652B GLY* 1.3 61.0 + - - +
653B SER* 3.4 18.9 + - - -
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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
------------------------------------------------------------
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