Contacts of the helix formed by residues 637 - 654 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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633A ASP 3.1 26.5 - - - -
634A ILE 3.2 6.7 + - - +
636A LYS* 1.3 89.7 - - + +
638A MET* 1.3 60.6 + - - +
639A VAL 3.1 2.6 + - - -
640A ILE* 3.4 13.5 + - + +
641A PHE* 3.0 26.6 + - - +
718A VAL* 5.1 11.7 - - + +
721A ASN* 3.9 25.1 - - - -
722A MET* 3.9 41.3 - - + -
725A ALA* 3.8 27.6 - - + -
726A MET* 5.0 4.3 - - + -
623D LEU* 4.0 26.9 - - + -
626D SER* 5.2 3.4 - - - -
627D LEU* 5.7 2.2 - - + -
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Residues in contact with MET 638 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634A ILE* 3.0 43.7 + - + +
635A PHE* 4.0 32.5 - - + +
636A LYS 3.5 0.4 - - - -
637A PHE* 1.3 77.0 - - - +
639A VAL* 1.3 56.8 + - + +
641A PHE* 3.7 11.7 - - + -
642A ILE* 2.9 38.3 + - + +
1003A SBJ 5.6 10.8 - - + -
713B VAL* 5.0 15.5 - - + -
717B ILE* 5.1 2.0 - - + -
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Residues in contact with VAL 639 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635A PHE 3.9 15.5 - - - +
636A LYS* 4.0 1.6 - - - +
637A PHE 3.1 0.8 - - - -
638A MET* 1.3 74.1 - - + +
640A ILE* 1.3 60.2 + - - +
642A ILE* 3.2 15.6 - - + +
643A MET* 3.0 52.6 + - + +
620D PHE* 3.7 42.6 - - + -
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Residues in contact with ILE 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636A LYS 4.9 6.3 - - - +
637A PHE* 3.4 12.8 + - + +
639A VAL* 1.3 74.9 - - + +
641A PHE* 1.3 65.1 + - - +
643A MET* 3.3 19.6 + - + +
644A VAL* 3.1 34.0 + - + +
718A VAL* 4.9 9.4 - - + -
614D LEU* 4.8 15.9 - - + -
620D PHE* 5.1 4.9 - - + -
623D LEU* 4.2 29.6 - - + -
624D GLN 5.0 0.2 - - - +
627D LEU* 4.0 32.3 - - + -
1003D S9Y 4.8 20.6 - - + +
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Residues in contact with PHE 641 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637A PHE* 3.0 17.1 + - + +
638A MET* 3.5 15.3 - - + +
639A VAL 3.2 0.2 - - - -
640A ILE* 1.3 77.2 - - - +
642A ILE* 1.3 62.4 + - + +
644A VAL* 3.4 0.8 + - - -
645A PHE* 2.9 35.6 + + - +
682A ILE* 3.7 41.3 - - + -
715A MET* 3.5 36.6 - - + +
718A VAL* 4.0 20.1 - - + +
719A LEU* 3.6 31.4 - - + -
722A MET* 6.4 0.9 - - - -
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Residues in contact with ILE 642 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A MET* 2.9 23.9 + - + +
639A VAL* 3.2 21.8 - - + +
641A PHE* 1.3 78.7 - - + +
643A MET* 1.3 61.8 + - + +
645A PHE* 3.9 9.4 - - + -
646A VAL* 2.9 39.3 + - + +
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Residues in contact with MET 643 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639A VAL* 3.0 42.4 + - + +
640A ILE* 3.3 16.1 + - + +
642A ILE* 1.3 78.3 - - + +
644A VAL* 1.3 62.5 + - - +
646A VAL* 4.0 3.4 - - - +
647A ALA* 3.0 25.6 + - - +
607D PHE* 4.6 5.6 - - + -
610D ILE* 3.7 38.4 - - + -
614D LEU* 4.0 30.3 - - + -
620D PHE* 5.9 0.9 - - + -
1003D S9Y 4.6 21.9 - - + +
1004D Y01 4.8 12.3 - - + -
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Residues in contact with VAL 644 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640A ILE* 3.1 23.3 + - + +
641A PHE* 5.0 0.4 - - - -
643A MET* 1.3 75.0 - - - +
645A PHE* 1.3 63.0 + - - +
647A ALA* 3.4 0.5 + - - +
648A PHE* 3.1 54.6 + - + +
711A TYR* 4.9 1.3 - - + -
714A THR* 3.8 26.5 - - + -
715A MET* 3.7 22.2 - - + -
718A VAL* 4.9 8.5 - - + -
1003D S9Y 3.8 31.2 - - + -
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Residues in contact with PHE 645 (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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641A PHE* 2.9 28.1 + + + +
642A ILE* 3.8 11.9 - - + +
643A MET 3.3 0.2 - - - -
644A VAL* 1.3 76.6 - - - +
646A VAL* 1.3 61.8 + - + +
648A PHE 3.5 0.3 + - - -
649A MET* 2.9 41.9 + - + +
675A PHE* 3.4 37.0 - + - -
678A LEU* 3.3 30.8 - - + +
679A PHE* 3.4 34.5 - + + -
682A ILE* 4.3 7.0 - - + -
711A TYR* 3.4 17.3 - + - -
715A MET* 3.9 10.5 - - + +
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Residues in contact with VAL 646 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642A ILE* 2.9 27.6 + - + +
643A MET* 4.0 3.4 - - - +
645A PHE* 1.3 75.8 - - + +
647A ALA* 1.3 66.4 + - - +
649A MET* 4.2 19.3 - - + -
650A ILE* 3.0 45.5 + - + +
607D PHE* 4.1 16.4 - - + -
1004D Y01 4.2 11.4 - - + -
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Residues in contact with ALA 647 (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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643A MET 3.0 18.3 + - - +
644A VAL* 3.5 8.7 - - - +
646A VAL* 1.3 77.0 - - - +
648A PHE* 1.3 60.5 + - + +
650A ILE* 3.5 1.6 + - - +
651A GLY* 3.0 25.8 + - - -
603D VAL 5.0 0.3 - - - +
604D VAL* 3.9 16.2 - - - +
607D PHE* 3.7 40.6 - - + -
1003D S9Y 4.6 9.0 - - + -
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Residues in contact with PHE 648 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644A VAL* 3.1 44.0 + - + +
645A PHE 4.3 0.2 - - - +
647A ALA* 1.3 80.4 - - + +
649A MET* 1.3 59.1 + - - +
652A MET* 3.0 39.9 + - + +
678A LEU* 3.7 16.9 - - + +
707A LEU* 3.6 34.1 - - + -
710A VAL* 3.7 27.1 - - + -
711A TYR* 3.8 26.5 - + + -
714A THR* 4.5 3.8 - - - -
604D VAL* 3.8 31.4 - - + -
1003D S9Y 4.0 18.6 - - + -
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Residues in contact with MET 649 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645A PHE* 2.9 24.3 + - + +
646A VAL* 3.7 23.3 - - + +
648A PHE* 1.3 77.5 - - - +
650A ILE* 1.3 71.9 + - + +
653A PHE* 3.0 27.9 + - + +
671A VAL* 4.3 21.1 - - + +
674A SER* 3.1 34.0 + - - +
675A PHE* 3.7 37.0 - - + -
678A LEU* 3.5 10.7 - - + +
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Residues in contact with ILE 650 (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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646A VAL* 3.0 39.4 + - + +
647A ALA 4.2 1.8 - - - +
649A MET* 1.3 88.1 - - + +
651A GLY* 1.3 57.8 + - - +
653A PHE* 3.4 10.2 + - + +
654A ASN* 3.0 40.9 + - - +
671A VAL* 6.5 0.7 - - + -
457D LEU 4.4 12.6 - - - +
458D VAL* 3.7 34.1 - - + -
603D VAL* 3.8 18.6 - - + -
607D PHE* 4.3 10.5 - - + -
1004D Y01 4.8 0.4 - - + -
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Residues in contact with GLY 651 (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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647A ALA 3.0 11.1 + - - -
648A PHE 3.9 0.2 - - - -
649A MET 3.3 0.2 - - - -
650A ILE* 1.3 79.1 - - - +
652A MET* 1.3 59.8 + - - +
654A ASN* 3.8 1.5 + - - +
655A LEU 3.5 6.2 + - - -
707A LEU* 4.4 1.0 - - - +
600D ALA* 3.3 28.4 - - - +
603D VAL* 3.8 14.1 - - - +
604D VAL* 3.7 26.9 - - - -
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Residues in contact with MET 652 (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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648A PHE* 3.0 22.8 + - + +
649A MET 4.4 0.7 - - - +
651A GLY* 1.3 74.5 - - - +
653A PHE* 1.3 60.7 + - - +
654A ASN 3.3 0.4 - - - -
655A LEU* 3.2 7.4 + - + +
656A TYR* 3.0 36.3 + - + +
668A PHE* 3.8 35.2 - - + +
678A LEU* 3.8 29.6 - - + -
691A VAL* 5.3 0.4 - - - -
704A GLY* 4.3 11.0 - - - +
707A LEU* 3.9 32.8 - - + +
708A TYR* 3.9 33.0 - - + +
711A TYR* 4.6 5.4 - - + -
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Residues in contact with PHE 653 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649A MET* 3.0 21.2 + - + +
650A ILE* 3.9 10.8 - - + +
652A MET* 1.3 78.3 - - - +
654A ASN* 1.3 76.6 + - - +
657A SER* 3.2 32.9 + - - -
668A PHE 3.9 7.2 - - - -
669A THR 3.5 28.3 - - - -
670A THR 4.2 2.7 - - - -
671A VAL* 4.0 20.0 - - + -
674A SER* 4.1 12.4 + - - +
461D ALA* 3.6 23.6 - - + -
464D ARG* 3.2 39.3 - - + -
465D PHE* 4.0 17.3 - + - -
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Residues in contact with ASN 654 (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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650A ILE* 3.0 28.1 + - - +
651A GLY* 4.0 6.1 - - - +
653A PHE* 1.3 91.5 - - - +
655A LEU* 1.3 60.0 + - - +
657A SER* 4.5 2.1 + - - -
658A TYR* 5.2 5.7 - - - -
457D LEU 4.3 10.0 + - - +
460D ASN* 6.2 0.2 - - - +
461D ALA* 3.6 19.6 - - - +
464D ARG* 4.3 14.1 + - - +
596D GLU* 4.7 9.1 - - - +
599D TYR* 3.5 36.2 + - + -
600D ALA* 5.0 5.8 - - - -
603D VAL* 3.9 16.4 - - - +
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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
------------------------------------------------------------
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