Contacts of the helix formed by residues 643 - 655 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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556C VAL* 4.0 2.4 - - - +
557C LEU* 3.7 25.8 - - + -
560C ASP* 2.6 30.1 - - - +
637C LEU* 2.8 19.1 + - + +
641C MET* 4.2 6.5 - - + -
642C GLY* 1.3 74.8 - - - +
644C LEU* 1.3 61.5 + - - +
645C TYR* 3.4 3.5 + - - +
646C SER* 3.1 22.7 + - - -
647C PHE* 3.2 19.6 + - - +
707C VAL* 3.3 27.0 - - - +
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Residues in contact with LEU 644 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638C LYS* 5.0 5.8 - - - -
642C GLY* 4.3 8.1 - - - +
643C ASP* 1.3 73.3 - - - +
645C TYR* 1.3 55.9 + - - +
647C PHE* 3.3 8.8 - - + +
648C SER* 2.8 36.4 + - - -
687C PHE* 4.3 15.9 - - + -
691C LEU* 4.4 12.8 - - + -
696C GLU* 3.7 35.9 - - + +
701C PRO* 4.2 25.4 - - + -
705C VAL* 3.9 25.6 - - + -
707C VAL 3.0 15.7 + - - +
709C LEU* 3.6 16.9 - - + +
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Residues in contact with TYR 645 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560C ASP* 3.5 35.4 - - + -
563C VAL* 5.6 1.1 - - + +
598C ILE* 2.8 47.2 + - + +
601C ARG* 3.1 29.5 - - + +
602C HIS* 3.4 31.5 + + + -
605C MET* 5.7 0.2 - - + -
643C ASP* 3.6 5.6 - - - +
644C LEU* 1.3 76.0 - - - +
646C SER* 1.3 73.4 + - - +
648C SER* 2.8 21.1 + - - -
649C ALA 3.1 4.7 + - - -
707C VAL* 3.6 9.4 - - + -
708C PRO 3.3 18.6 + - - +
709C LEU 3.5 20.2 - - - +
710C LEU* 4.2 11.9 - - + -
711C MET* 4.2 2.7 - - + -
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Residues in contact with SER 646 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556C VAL* 3.3 19.6 - - - +
560C ASP* 2.4 31.3 + - - -
605C MET* 3.2 22.8 - - - +
637C LEU* 4.0 7.6 - - - -
643C ASP* 3.1 9.9 + - - -
645C TYR* 1.3 78.8 - - - +
647C PHE* 1.3 66.5 + - - +
649C ALA* 3.2 9.8 + - - +
650C LEU* 3.2 25.6 + - - +
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Residues in contact with PHE 647 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634C ALA* 3.4 28.9 - - + +
637C LEU* 4.0 12.8 - - + +
638C LYS* 3.9 17.0 - - + +
643C ASP 3.2 21.1 + - - +
644C LEU* 3.3 9.9 - - + +
646C SER* 1.3 77.1 - - - +
648C SER* 1.3 67.5 + - - +
650C LEU* 3.1 14.6 + - - +
651C MET* 3.2 42.2 + - + +
684C LEU* 4.0 28.7 - - + -
687C PHE* 3.7 31.9 - + - -
688C SER* 4.4 8.7 - - - -
691C LEU* 4.2 15.5 - - + -
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Residues in contact with SER 648 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602C HIS* 2.7 30.2 + - - -
644C LEU 2.8 10.4 + - - -
645C TYR* 2.8 8.9 + - - -
647C PHE* 1.3 80.1 - - - +
649C ALA* 1.3 56.8 + - - +
651C MET* 3.3 6.8 + - - +
652C LYS* 2.9 31.0 + - - +
688C SER* 5.8 2.5 - - - -
691C LEU* 5.5 0.4 - - - -
709C LEU* 3.3 34.5 + - - +
711C MET* 4.6 2.1 - - - +
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Residues in contact with ALA 649 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602C HIS* 3.4 35.7 - - + +
605C MET* 3.9 29.8 - - + -
606C ALA* 3.6 16.8 - - - +
645C TYR 3.1 3.0 + - - +
646C SER* 3.4 10.8 - - - +
647C PHE 3.2 0.2 - - - -
648C SER* 1.3 82.1 + - - +
650C LEU* 1.3 62.2 + - - +
652C LYS* 3.4 1.3 + - - +
653C ALA* 3.2 16.6 + - - +
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Residues in contact with LEU 650 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556C VAL* 6.4 0.2 - - + -
605C MET* 4.7 8.3 - - - -
609C ILE* 3.8 31.4 - - + +
630C ILE* 3.4 36.3 - - + +
633C VAL* 3.9 17.7 - - + -
634C ALA* 3.7 25.8 - - + +
637C LEU* 4.2 8.1 - - + -
646C SER 3.4 13.0 - - - +
647C PHE 3.1 8.5 + - - +
649C ALA* 1.3 76.0 - - + +
651C MET* 1.3 65.9 + - - +
653C ALA* 3.1 10.1 + - - +
654C LEU* 3.0 26.9 + - + +
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Residues in contact with MET 651 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634C ALA* 4.7 4.3 - - - -
647C PHE* 3.2 44.3 + - + +
648C SER* 3.7 8.7 - - - +
650C LEU* 1.3 76.6 - - - +
652C LYS* 1.3 63.4 + - - +
654C LEU* 3.2 10.9 + - - +
655C GLU* 3.1 34.9 + - - +
680C TYR* 3.5 33.7 - - + +
684C LEU* 3.5 42.4 - - + +
685C LYS* 3.7 10.5 - - + +
688C SER* 4.1 15.3 - - - +
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Residues in contact with LYS 652 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602C HIS* 4.5 15.0 - - + +
603C ASN* 3.6 15.0 + - - -
606C ALA* 3.8 19.4 - - + +
648C SER 2.9 17.8 + - - +
649C ALA* 3.6 6.3 - - - +
651C MET* 1.3 75.3 - - - +
653C ALA* 1.3 63.5 + - - +
655C GLU* 3.1 19.4 + - + +
656C MET* 3.2 23.0 + - + +
724C PHE* 2.9 45.4 + - - +
725C GLU* 5.3 1.3 - - - -
727C THR* 2.8 37.8 + - + +
728C ASP* 5.7 0.7 - - - +
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Residues in contact with ALA 653 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606C ALA* 3.7 12.4 - - - +
609C ILE* 3.6 34.3 - - + -
610C ALA* 4.0 7.2 - - - +
613C ILE* 5.5 1.1 - - + -
649C ALA 3.2 6.8 + - - +
650C LEU 3.1 10.6 + - - +
652C LYS* 1.3 78.3 - - - +
654C LEU* 1.3 58.3 + - + +
656C MET* 3.0 31.3 + - - +
659C ILE* 3.4 19.5 - - - +
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Residues in contact with LEU 654 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613C ILE* 4.0 14.8 - - + -
627C LEU* 3.4 32.1 - - + -
630C ILE* 4.2 17.3 - - + +
631C ILE* 3.8 23.6 - - + -
634C ALA* 5.6 0.9 - - + -
650C LEU* 3.0 18.2 + - + +
651C MET* 3.2 11.6 + - - +
653C ALA* 1.3 75.6 - - + +
655C GLU* 1.3 58.5 + - - +
656C MET 3.5 0.4 - - - -
659C ILE* 4.1 9.1 - - + +
660C THR* 4.5 6.9 + - - -
666C TRP* 3.8 19.9 - - + -
680C TYR* 3.5 41.2 + - + +
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Residues in contact with GLU 655 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651C MET* 3.1 29.1 + - - +
652C LYS* 3.1 9.9 + - + +
653C ALA 3.0 1.2 - - - -
654C LEU* 1.3 79.2 - - - +
656C MET* 1.3 65.6 + - - +
657C PRO* 3.4 5.9 - - - +
660C THR* 4.4 8.7 - - - +
680C TYR* 4.1 11.9 + - - +
685C LYS* 5.0 12.3 - - - +
688C SER* 4.2 15.2 + - - -
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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