Contacts of the helix formed by residues 637 - 654 (chain B) in PDB entry 6UZA
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 PHE 637 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623A LEU* 4.0 28.0 - - + -
626A SER* 5.2 3.6 - - - -
627A LEU* 5.7 3.1 - - + -
633B ASP* 3.1 27.6 - - + -
634B ILE 3.2 5.6 + - - +
636B LYS* 1.3 88.8 - - + +
638B MET* 1.3 60.3 + - - +
639B VAL 3.1 2.2 + - - -
640B ILE* 3.4 13.7 + - + +
641B PHE* 3.0 27.2 + - - +
718B VAL* 5.1 10.7 - - + +
721B ASN* 3.9 24.2 - - - -
722B MET* 3.9 42.8 - - + -
725B ALA* 3.8 27.6 - - + -
726B MET* 5.0 3.4 - - + -
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Residues in contact with MET 638 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634B ILE* 3.0 45.2 + - + +
635B PHE* 4.0 33.0 - - + +
636B LYS 3.5 0.4 - - - -
637B PHE* 1.3 76.8 - - - +
639B VAL* 1.3 56.1 + - - +
641B PHE* 3.5 10.9 - - + +
642B ILE* 2.9 38.0 + - + +
1004B SBJ 5.6 10.1 - - + -
713C VAL* 5.0 15.3 - - + -
717C ILE* 5.1 1.8 - - + -
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Residues in contact with VAL 639 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620A PHE* 3.7 43.3 - - + -
635B PHE 3.9 15.0 - - - +
636B LYS 4.0 1.6 - - - +
637B PHE 3.1 1.2 - - - -
638B MET* 1.3 75.2 - - + +
640B ILE* 1.3 60.5 + - - +
642B ILE* 3.2 15.5 - - + +
643B MET* 3.0 52.6 + - + +
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Residues in contact with ILE 640 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614A LEU* 4.8 16.8 - - + -
620A PHE* 5.1 4.5 - - + -
623A LEU* 4.2 29.6 - - + -
624A GLN 5.0 0.2 - - - +
627A LEU* 4.0 32.5 - - + -
1002A S9Y 4.8 19.3 - - + +
636B LYS 4.9 6.5 - - - +
637B PHE* 3.4 12.8 + - + +
639B VAL* 1.3 74.4 - - + +
641B PHE* 1.3 65.3 + - - +
643B MET* 3.3 18.1 + - + +
644B VAL* 3.1 33.6 + - + +
718B VAL* 4.9 10.5 - - + -
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Residues in contact with PHE 641 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637B PHE* 3.0 17.3 + - + +
638B MET* 3.5 14.1 - - + +
639B VAL 3.2 0.2 - - - -
640B ILE* 1.3 78.0 - - - +
642B ILE* 1.3 61.8 + - + +
644B VAL* 3.4 1.1 + - - -
645B PHE* 2.9 36.3 + + + +
682B ILE* 3.7 40.4 - - + -
715B MET* 3.5 36.3 - - + +
718B VAL* 4.0 22.1 - - + +
719B LEU* 3.6 30.7 - - + -
722B MET* 6.4 0.9 - - - -
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Residues in contact with ILE 642 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638B MET* 2.9 25.7 + - + +
639B VAL* 3.2 21.8 - - + +
641B PHE* 1.3 79.1 - - + +
643B MET* 1.3 60.5 + - + +
645B PHE* 3.9 9.2 - - + -
646B VAL* 2.9 39.5 + - + +
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Residues in contact with MET 643 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607A PHE* 4.6 5.9 - - + -
610A ILE* 3.7 38.4 - - + -
614A LEU* 4.0 29.4 - - + -
620A PHE* 5.9 0.9 - - + -
1002A S9Y 4.6 22.1 - - + +
1004A Y01 4.8 12.6 - - + -
639B VAL* 3.0 41.8 + - + +
640B ILE* 3.3 15.7 + - + +
642B ILE* 1.3 78.7 - - + +
644B VAL* 1.3 62.5 + - - +
646B VAL* 4.0 3.8 - - - +
647B ALA* 3.0 24.4 + - - +
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Residues in contact with VAL 644 (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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1002A S9Y 3.8 32.3 - - + -
640B ILE* 3.1 23.3 + - + +
641B PHE* 5.0 0.2 - - - -
643B MET* 1.3 75.1 - - - +
645B PHE* 1.3 63.1 + - - +
647B ALA* 3.4 0.9 + - - +
648B PHE* 3.1 55.4 + - + +
711B TYR* 4.9 1.3 - - + -
714B THR* 3.8 25.1 - - + -
715B MET* 3.7 22.4 - - + -
718B VAL* 4.9 7.9 - - + -
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Residues in contact with PHE 645 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641B PHE* 2.9 28.3 + + + +
642B ILE* 3.8 11.0 - - + +
644B VAL* 1.3 78.1 - - - +
646B VAL* 1.3 61.6 + - + +
648B PHE* 3.9 0.5 - - - -
649B MET* 2.9 42.1 + - + +
675B PHE* 3.4 38.4 - + - -
678B LEU* 3.3 31.3 - - + +
679B PHE* 3.4 34.8 - + + -
682B ILE* 4.3 6.7 - - + -
711B TYR* 3.4 16.2 - + - -
715B MET* 3.9 10.9 - - + +
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Residues in contact with VAL 646 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607A PHE* 4.1 15.7 - - + -
1004A Y01 4.2 11.2 - - + -
642B ILE* 2.9 27.5 + - + +
643B MET* 4.0 3.8 - - - +
645B PHE* 1.3 75.8 - - + +
647B ALA* 1.3 65.6 + - - +
649B MET* 4.2 18.6 - - + -
650B ILE* 3.0 46.7 + - + +
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Residues in contact with ALA 647 (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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603A VAL 5.0 0.2 - - - +
604A VAL* 3.9 15.5 - - - +
607A PHE* 3.7 40.5 - - + -
1002A S9Y 4.6 9.2 - - + -
643B MET 3.0 18.5 + - - +
644B VAL* 3.5 8.3 - - - +
645B PHE 3.3 0.2 - - - -
646B VAL* 1.3 78.5 - - - +
648B PHE* 1.3 61.6 + - + +
650B ILE* 4.0 1.6 - - - +
651B GLY* 3.0 25.6 + - - -
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Residues in contact with PHE 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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604A VAL* 3.8 30.1 - - + -
1002A S9Y 4.0 20.0 - - + -
644B VAL* 3.1 45.1 + - + +
647B ALA* 1.3 79.3 - - + +
649B MET* 1.3 60.7 + - - +
652B MET* 3.0 39.5 + - + +
678B LEU* 3.7 18.2 - - + +
707B LEU* 3.6 34.3 - - + -
710B VAL* 3.7 26.5 - - + -
711B TYR* 3.8 24.7 - + + -
714B THR* 4.5 3.4 - - - -
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Residues in contact with MET 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 PHE* 2.9 25.3 + - + +
646B VAL* 3.7 23.1 - - + +
648B PHE* 1.3 76.5 - - - +
650B ILE* 1.3 71.2 + - + +
653B PHE* 3.0 27.7 + - + +
671B VAL* 4.3 20.6 - - + +
674B SER* 3.1 33.6 + - - +
675B PHE* 3.7 36.8 - - + +
678B LEU* 3.5 11.1 - - + +
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Residues in contact with ILE 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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457A LEU 4.4 12.1 - - - +
458A VAL* 3.7 33.4 - - + -
603A VAL* 3.8 18.4 - - + -
607A PHE* 4.3 10.8 - - + -
1004A Y01 4.8 0.4 - - + -
646B VAL* 3.0 39.2 + - + +
647B ALA 4.2 1.1 - - - +
649B MET* 1.3 86.2 - - + +
651B GLY* 1.3 58.5 + - - +
653B PHE* 3.4 9.9 + - + +
654B ASN* 3.0 41.8 + - - +
671B VAL* 6.5 0.9 - - + -
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Residues in contact with GLY 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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600A ALA* 3.3 28.0 - - - +
603A VAL* 3.8 14.5 - - - +
604A VAL* 3.7 26.9 - - - -
647B ALA 3.0 11.5 + - - -
648B PHE 3.8 0.2 - - - -
650B ILE* 1.3 78.0 - - - +
652B MET* 1.3 59.3 + - - +
654B ASN* 3.8 1.5 + - - +
655B LEU* 3.5 6.1 + - - +
707B LEU* 4.4 0.8 - - - +
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Residues in contact with MET 652 (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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648B PHE* 3.0 24.4 + - + +
649B MET 4.4 0.7 - - - +
651B GLY* 1.3 74.5 - - - +
653B PHE* 1.3 62.1 + - - +
654B ASN 3.3 0.2 - - - -
655B LEU* 3.2 7.2 + - + +
656B TYR* 3.0 35.8 + - + +
668B PHE* 3.8 36.1 - - + +
674B SER* 5.0 0.2 - - - +
678B LEU* 3.8 28.7 - - + -
691B VAL* 5.3 0.2 - - - -
704B GLY* 4.3 11.7 - - - +
707B LEU* 3.9 33.0 - - + +
708B TYR* 3.9 33.7 - - + +
711B TYR* 4.6 5.2 - - + -
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Residues in contact with PHE 653 (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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461A ALA* 3.6 22.4 - - + -
464A ARG* 3.2 40.2 - - + -
465A PHE* 4.0 16.8 - + - -
649B MET* 3.0 20.5 + - + +
650B ILE* 3.9 10.3 - - + +
652B MET* 1.3 78.1 - - - +
654B ASN* 1.3 75.4 + - - +
657B SER* 3.2 33.0 + - - -
668B PHE 3.9 7.2 - - - -
669B THR 3.5 26.5 - - - -
670B THR 4.2 2.9 - - - -
671B VAL* 4.0 20.2 - - + -
674B SER* 4.1 13.1 + - - +
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Residues in contact with ASN 654 (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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457A LEU 4.3 9.2 + - - +
460A ASN* 5.9 0.4 - - - +
461A ALA* 3.6 19.1 - - - +
464A ARG* 4.3 15.0 + - - +
596A GLU* 4.7 8.7 - - - +
599A TYR* 3.5 37.3 + - + -
600A ALA* 5.0 5.2 - - - -
603A VAL* 3.9 16.2 - - - +
650B ILE* 3.0 27.3 + - - +
651B GLY* 4.0 6.1 - - - +
652B MET 3.3 0.2 - - - -
653B PHE* 1.3 93.7 - - - +
655B LEU* 1.3 59.8 + - - +
657B SER* 4.5 2.5 + - - -
658B TYR* 5.2 5.9 - - - -
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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