Contacts of the helix formed by residues 639 - 656 (chain A) in PDB entry 5W6V
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 639 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610A THR* 5.4 0.6 + - - +
628A ARG* 3.5 49.1 - - + +
629A VAL 4.4 7.8 - - - +
630A GLN* 4.8 3.6 + - - +
637A ILE* 3.3 2.4 - - - +
638A GLU* 1.3 81.0 - - - +
640A LEU* 1.3 62.8 + - - +
641A SER* 3.2 3.7 + - - -
642A TYR* 3.3 8.0 + - + +
643A MET* 3.1 25.0 + - - +
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Residues in contact with LEU 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A VAL* 3.6 29.6 - - + -
637A ILE* 3.1 28.7 + - + +
638A GLU 3.2 2.2 + - - -
639A ASP* 1.3 77.0 - - - +
641A SER* 1.3 63.4 + - - +
643A MET* 4.3 2.9 - - + -
644A VAL* 2.9 41.5 + - + +
664A PHE* 4.2 17.9 - - + -
681A GLU* 3.5 48.9 - - + +
684A ALA* 4.1 9.2 - - + -
685A ILE* 4.0 9.2 - - + -
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Residues in contact with SER 641 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A GLU 4.7 2.5 + - - -
639A ASP 3.2 1.0 - - - -
640A LEU* 1.3 79.7 - - - +
642A TYR* 1.3 58.8 + - - +
645A ARG* 3.2 20.4 + - - +
684A ALA* 3.4 33.5 + - - +
687A ASP* 3.1 25.0 + - - -
688A ALA* 3.2 20.6 + - - +
691A LYS* 4.4 3.0 + - - -
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Residues in contact with TYR 642 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628A ARG* 3.8 18.6 - - - +
639A ASP* 3.3 10.8 + - + +
640A LEU 3.3 0.2 - - - -
641A SER* 1.3 77.4 - - - +
643A MET* 1.3 65.7 + - - +
645A ARG* 3.2 33.6 + - - +
646A GLU* 3.0 43.4 + - + +
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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
----------------------------------------------------------
610A THR* 3.9 18.6 - - - +
611A ALA 4.0 0.4 - - - -
612A VAL* 3.5 42.4 - - + +
626A THR* 3.6 25.9 + - - +
627A VAL* 4.2 2.2 - - - +
628A ARG* 3.6 36.8 - - - +
637A ILE* 3.9 13.5 - - + -
639A ASP* 3.1 26.9 + - - +
640A LEU* 3.8 3.8 - - - +
642A TYR* 1.3 77.6 - - - +
644A VAL* 1.3 62.0 + - - +
646A GLU* 3.4 9.7 + - - +
647A LEU* 3.2 28.1 + - - +
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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
----------------------------------------------------------
592A LEU* 4.0 26.5 - - + -
612A VAL* 4.9 2.2 - - + -
640A LEU* 2.9 42.1 + - + +
641A SER* 3.9 4.3 - - - +
643A MET* 1.3 73.7 - - - +
645A ARG* 1.3 61.1 + - - +
647A LEU* 3.2 7.5 + - - +
648A LEU* 2.9 49.8 + - + +
662A ILE* 5.3 2.2 - - + -
664A PHE* 5.0 0.2 - - + -
685A ILE* 4.4 25.4 - - + -
688A ALA* 3.9 11.7 - - + -
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Residues in contact with ARG 645 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641A SER 3.2 16.2 + - - +
642A TYR* 3.2 42.6 + - + +
644A VAL* 1.3 76.6 - - - +
646A GLU* 1.3 62.6 + - + +
648A LEU* 3.3 7.9 + - - +
649A ILE* 3.0 47.0 + - + +
688A ALA* 4.1 12.7 + - + +
691A LYS* 3.4 31.5 + - - +
692A LEU* 3.4 33.6 - - + +
838B TRP 6.2 1.2 - - - -
839B GLY 6.0 1.2 - - - -
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Residues in contact with GLU 646 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626A THR* 3.5 24.6 - - + +
628A ARG* 2.9 31.6 + - - -
642A TYR* 3.0 38.7 + - + +
643A MET* 3.8 4.7 - - - +
644A VAL 3.3 0.2 - - - -
645A ARG* 1.3 76.6 - - + +
647A LEU* 1.3 58.7 + - - +
649A ILE* 3.3 8.8 + - + +
650A GLN* 2.9 34.6 + - + +
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Residues in contact with LEU 647 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590A ILE* 4.1 4.2 - - + +
592A LEU* 3.7 17.0 - - + -
612A VAL* 3.6 29.4 - - + +
613A VAL 3.5 24.2 - - - +
614A GLY* 3.6 6.5 - - - +
616A MET* 3.6 12.4 - - + +
624A CYS* 3.3 36.6 - - + +
626A THR* 4.1 16.2 - - + +
643A MET 3.2 13.4 + - - +
644A VAL* 3.2 6.7 + - + +
646A GLU* 1.3 74.9 - - - +
648A LEU* 1.3 61.2 + - + +
650A GLN* 3.3 1.7 + - - -
651A PHE* 2.9 30.7 + - - +
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Residues in contact with LEU 648 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590A ILE* 4.3 16.8 - - + -
592A LEU* 6.3 1.3 - - + -
644A VAL* 2.9 39.8 + - + +
645A ARG* 3.7 5.4 - - - +
647A LEU* 1.3 75.7 - - + +
649A ILE* 1.3 58.3 + - - +
651A PHE* 3.5 4.9 + - - +
652A TYR 3.0 21.7 + - - -
659A PRO* 4.0 25.6 - - + -
662A ILE* 4.4 9.4 - - + -
688A ALA* 4.7 4.3 - - + -
689A CYS* 4.2 21.1 - - - +
692A LEU* 3.7 27.1 - - + -
696A TYR* 4.2 10.5 - - + +
838B TRP* 3.5 15.0 - - + -
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Residues in contact with ILE 649 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645A ARG* 3.0 48.2 + - + +
646A GLU* 3.7 7.2 - - - +
647A LEU 3.2 0.2 - - - -
648A LEU* 1.3 75.2 - - - +
650A GLN* 1.3 67.3 + - + +
652A TYR* 3.2 4.0 + - + +
653A LYS* 3.0 36.6 + - + +
692A LEU* 4.1 20.6 - - + -
838B TRP* 4.5 6.7 - - + -
839B GLY* 3.7 44.6 - - - +
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Residues in contact with GLN 650 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A MET* 3.5 19.4 - - + +
622A ARG* 5.6 1.9 + - - -
624A CYS* 4.2 20.8 - - - -
646A GLU* 2.9 20.8 + - + +
647A LEU* 3.3 3.3 + - + +
649A ILE* 1.3 75.7 - - + +
651A PHE* 1.3 64.9 + - - +
653A LYS* 3.2 25.7 + - - +
654A SER* 2.9 33.4 + - - -
851A LEU* 5.7 9.6 - - - +
852A ARG* 5.2 13.4 - - - +
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Residues in contact with PHE 651 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A PRO* 4.6 0.2 - - + -
589A VAL 3.5 28.3 - - - -
590A ILE* 3.9 16.4 - - + -
615A SER* 3.1 24.9 - - - -
616A MET* 3.4 13.5 - - + -
617A ASP 4.4 10.3 - - - -
647A LEU 2.9 18.4 + - - +
648A LEU* 3.6 5.8 - - - +
650A GLN* 1.3 75.9 - - - +
652A TYR* 1.3 55.5 + - - +
654A SER* 3.3 2.0 + - - -
655A THR* 3.0 50.4 + - + +
657A PHE* 3.3 28.5 - - + -
659A PRO* 3.5 29.2 - - + -
828B TRP* 3.9 19.3 - + - -
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Residues in contact with TYR 652 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648A LEU 3.0 8.6 + - - +
649A ILE 3.6 4.9 - - - +
650A GLN 3.2 0.2 - - - -
651A PHE* 1.3 77.6 - - - +
653A LYS* 1.3 62.3 + - + +
656A ARG* 2.9 44.6 + - + +
657A PHE 3.5 21.3 - - - +
658A LYS* 3.7 29.4 - - + -
832B ILE 5.0 7.9 + - - -
835B GLY 4.8 3.5 + - - -
836B PRO 4.1 2.6 + - - -
837B SER* 3.1 44.6 + - - -
838B TRP* 3.5 33.7 - + + -
839B GLY* 4.7 2.7 - - - -
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Residues in contact with LYS 653 (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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649A ILE* 3.0 38.0 + - + +
650A GLN* 3.2 26.8 + - - +
652A TYR* 1.3 83.9 - - + +
654A SER* 1.3 62.2 + - - +
656A ARG* 4.4 8.2 + - - +
839B GLY* 4.1 19.1 + - - -
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Residues in contact with SER 654 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A MET* 3.5 22.0 - - - +
622A ARG* 2.8 35.6 + - - -
650A GLN* 2.9 23.8 + - - -
651A PHE 3.9 2.0 - - - -
653A LYS* 1.3 79.7 - - - +
655A THR* 1.3 58.5 + - - +
656A ARG* 5.6 1.2 - - - -
852A ARG* 6.0 0.2 - - - +
825B THR* 4.3 8.5 - - - +
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Residues in contact with THR 655 (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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616A MET 3.4 27.6 - - - +
617A ASP* 4.5 1.6 - - - -
651A PHE* 3.0 33.6 + - + +
654A SER* 1.3 80.1 - - - +
656A ARG* 1.3 67.8 + - - +
657A PHE* 2.9 50.7 + - - +
825B THR* 3.7 20.0 - - + +
826B SER* 4.6 7.4 + - - -
828B TRP* 4.6 5.6 - - + -
831B PRO* 5.6 0.5 - - - +
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Residues in contact with ARG 656 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652A TYR* 2.9 35.2 + - + +
653A LYS* 4.8 7.2 - - - +
654A SER 5.8 0.9 - - - -
655A THR* 1.3 80.0 - - - +
657A PHE* 1.3 64.4 + - - +
831B PRO* 3.5 36.4 - - + +
832B ILE 4.6 15.6 + - - +
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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