Contacts of the helix formed by residues 643 - 656 (chain B) in PDB entry 3T6A
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 643 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556B VAL* 3.9 1.6 - - - +
557B LEU* 3.6 25.3 + - + -
560B ASP* 2.6 31.6 - - - +
637B LEU* 2.9 24.2 + - + +
641B MET* 4.1 2.2 - - + -
642B GLY* 1.3 74.4 - - - +
644B LEU* 1.3 63.5 + - - +
645B TYR* 3.4 9.4 + - - +
646B SER* 3.0 22.6 + - - -
647B PHE* 3.1 21.1 + - - +
707B VAL* 3.6 17.3 - - - +
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Residues in contact with LEU 644 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638B LYS* 5.2 5.6 - - - -
642B GLY* 4.8 5.8 - - - -
643B ASP* 1.3 70.8 - - - +
645B TYR* 1.3 66.5 + - - +
647B PHE* 3.6 6.9 - - + +
648B SER* 2.9 26.3 + - - -
687B PHE* 4.1 27.4 - - + -
691B LEU* 4.3 11.4 - - + -
696B GLU* 3.5 41.5 - - + +
701B PRO* 4.3 19.3 - - + -
705B VAL* 4.0 25.6 - - + -
707B VAL 2.8 15.2 + - - +
708B PRO 4.1 0.2 - - - -
709B LEU* 3.6 15.1 - - - +
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Residues in contact with TYR 645 (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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560B ASP* 3.6 35.7 - - + -
563B VAL* 6.3 0.7 - - + -
598B ILE* 2.6 50.0 + - + -
601B ARG* 3.3 20.7 - - + +
602B HIS* 3.1 41.0 + + + -
605B MET* 4.6 2.7 - - + -
643B ASP* 3.4 6.7 + - - +
644B LEU* 1.3 75.9 - - - +
646B SER* 1.3 61.3 + - - +
648B SER* 2.8 21.8 + - - -
649B ALA 3.3 3.5 + - - -
707B VAL* 3.7 7.6 - - + -
708B PRO 3.2 20.7 + - - +
709B LEU 3.5 18.8 - - - -
710B LEU* 4.0 13.9 - - + -
711B MET* 4.6 2.7 - - - -
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Residues in contact with SER 646 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556B VAL* 3.2 20.1 - - - +
560B ASP* 2.5 25.4 + - - -
605B MET* 3.2 29.2 - - - +
637B LEU* 3.9 8.7 - - - -
643B ASP* 3.0 13.8 + - - -
645B TYR* 1.3 72.1 - - - +
647B PHE* 1.3 66.6 + - - +
649B ALA* 3.1 14.2 + - - +
650B LEU* 3.2 19.4 + - - +
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Residues in contact with PHE 647 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634B ALA* 3.4 29.2 - - + +
637B LEU* 4.0 15.7 - - + +
638B LYS* 3.8 17.5 - - + +
643B ASP 3.1 20.9 + - - +
644B LEU* 3.6 6.3 - - + +
646B SER* 1.3 78.8 - - - +
648B SER* 1.3 66.6 + - - +
650B LEU* 3.5 3.4 + - - +
651B MET* 3.1 55.4 + - + +
684B LEU* 3.9 27.6 - - + -
687B PHE* 3.6 35.7 - + - -
688B SER* 4.6 7.0 - - - -
691B LEU* 4.1 18.4 - - + -
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Residues in contact with SER 648 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602B HIS* 2.8 29.1 + - - -
644B LEU 2.9 7.7 + - - -
645B TYR* 2.8 9.4 + - - -
647B PHE* 1.3 83.2 - - - +
649B ALA* 1.3 57.9 + - - +
651B MET* 3.7 6.0 - - - +
652B LYS* 2.9 30.3 + - - +
688B SER* 5.7 2.2 - - - -
691B LEU* 5.2 1.1 - - - -
709B LEU* 3.4 34.4 + - - +
711B MET* 4.8 1.6 - - - +
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Residues in contact with ALA 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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602B HIS* 3.5 39.5 - - + +
605B MET* 3.9 27.6 - - + -
606B ALA* 3.5 12.3 - - - +
645B TYR 3.3 3.6 + - - +
646B SER* 3.1 9.9 + - - +
648B SER* 1.3 80.6 + - - +
650B LEU* 1.3 63.7 + - - +
652B LYS* 3.2 12.1 + - - +
653B ALA* 3.3 10.0 + - - +
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Residues in contact with LEU 650 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556B VAL* 6.4 0.2 - - + -
605B MET* 4.3 15.3 - - - -
609B ILE* 3.8 37.3 - - + +
630B ILE* 3.9 20.9 - - + +
633B VAL* 3.8 12.1 - - + -
634B ALA* 3.8 25.6 - - + +
637B LEU* 3.8 25.4 - - + -
646B SER 3.2 12.8 + - - +
647B PHE 3.9 6.5 - - - +
649B ALA* 1.3 75.4 - - - +
651B MET* 1.3 63.2 + - - +
652B LYS 3.3 0.3 + - - -
653B ALA* 3.3 6.2 + - - +
654B LEU* 3.2 25.1 + - + +
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Residues in contact with MET 651 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634B ALA* 4.8 6.7 - - + -
647B PHE* 3.1 49.1 + - + +
648B SER* 3.7 6.3 - - - +
650B LEU* 1.3 75.6 - - - +
652B LYS* 1.3 62.0 + - - +
654B LEU* 3.2 9.4 + - - +
655B GLU* 3.2 35.9 + - - +
680B TYR* 3.7 33.6 + - + +
684B LEU* 3.7 38.1 - - + +
685B LYS* 4.0 6.7 - - + +
688B SER* 3.8 20.0 - - - +
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Residues in contact with LYS 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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602B HIS* 4.5 16.0 + - + -
603B ASN* 4.0 9.3 + - - +
606B ALA* 3.9 18.2 - - + +
648B SER 2.9 13.8 + - - +
649B ALA* 3.4 10.8 - - - +
650B LEU 3.2 0.4 - - - -
651B MET* 1.3 75.2 - - - +
653B ALA* 1.3 62.6 + - - +
655B GLU* 2.9 18.8 + - - +
656B MET* 3.0 18.0 + - + +
724B PHE* 2.8 44.5 + - - +
725B GLU* 5.4 2.0 - - - -
727B THR* 2.7 47.6 + - + +
728B ASP* 5.7 1.8 - - - +
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Residues in contact with ALA 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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606B ALA* 3.5 22.6 - - - +
609B ILE* 3.6 23.3 - - + -
610B ALA* 4.0 7.0 - - - +
613B ILE* 6.2 0.7 - - + -
649B ALA 3.3 5.8 + - - +
650B LEU 3.4 10.1 - - - +
652B LYS* 1.3 78.5 - - - +
654B LEU* 1.3 64.2 + - + +
656B MET* 3.1 33.6 + - + +
659B ILE* 3.4 13.1 - - - +
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Residues in contact with LEU 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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609B ILE* 5.1 0.2 - - + -
613B ILE* 3.9 15.5 - - + -
627B LEU* 3.2 31.2 - - + -
630B ILE* 4.1 18.4 - - + -
631B ILE* 3.8 24.0 - - + -
650B LEU* 3.2 14.5 + - + +
651B MET* 3.2 12.7 + - - +
653B ALA* 1.3 76.3 - - + +
655B GLU* 1.3 59.3 + - - +
656B MET 3.5 0.2 - - - -
659B ILE* 4.0 11.1 - - + +
660B THR* 4.5 6.6 + - - -
666B TRP* 3.8 19.1 - - + -
680B TYR* 3.7 38.2 + - + +
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Residues in contact with GLU 655 (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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651B MET* 3.2 25.4 + - - +
652B LYS* 2.9 11.6 + - - +
654B LEU* 1.3 77.1 - - - +
656B MET* 1.3 67.2 + - - +
657B PRO* 3.3 6.4 - - - +
660B THR* 4.4 9.1 - - - +
680B TYR* 4.1 11.2 - - - +
685B LYS* 4.7 15.9 - - - +
688B SER* 4.1 17.8 + - - -
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Residues in contact with MET 656 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606B ALA* 3.4 36.1 - - + +
607B ILE 4.3 0.2 - - - +
610B ALA* 3.6 21.3 - - + -
652B LYS* 3.0 17.0 + - + +
653B ALA* 3.1 26.0 + - - +
655B GLU* 1.3 76.8 - - - +
657B PRO* 1.3 57.9 - - - -
658B GLN* 3.5 11.9 - - - +
659B ILE* 2.7 30.6 + - + -
660B THR 2.8 13.7 + - - -
724B PHE* 3.6 33.4 - - + -
725B GLU* 3.2 16.2 - - - +
727B THR* 6.5 0.2 - - + -
808B LEU* 4.1 6.5 - - - -
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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