Contacts of the helix formed by residues 644 - 662 (chain C) in PDB entry 2W4V
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 THR 644 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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534C GLU* 1.6 39.7 + - + +
537C CYS* 3.6 29.4 - - - -
538C MET* 4.9 9.2 - - - -
598C ASN* 3.3 15.5 - - - +
599C LYS* 5.9 3.1 - - + +
643C GLN* 1.3 91.6 + - - +
645C ILE* 1.3 61.1 + - - +
647C ALA* 3.1 8.2 + - + +
648C VAL 2.9 19.6 + - - -
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Residues in contact with ILE 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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269C LYS* 5.9 4.7 - - - +
472C PHE* 3.0 36.6 - - + -
476C CYS* 4.6 2.5 - - - -
597C LYS 4.2 5.8 - - - +
598C ASN* 2.7 44.2 - - - +
599C LYS* 4.8 0.4 - - - -
600C ASP* 4.8 10.5 - - + +
643C GLN* 4.0 2.5 - - - +
644C THR* 1.3 73.5 - - - +
646C SER* 1.3 67.7 + - - +
648C VAL* 2.2 32.5 - - - +
649C HIS* 2.4 55.4 + - + +
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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
----------------------------------------------------------
472C PHE* 4.0 0.2 - - - -
530C LEU* 3.0 36.5 - - - +
534C GLU* 2.7 32.3 + - - -
598C ASN* 2.2 25.2 + - - -
644C THR* 3.6 0.2 + - - -
645C ILE* 1.3 90.0 - - - +
647C ALA* 1.3 55.3 + - - +
649C HIS* 4.0 1.5 - - - +
650C ARG* 2.8 33.4 + - - +
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Residues in contact with ALA 647 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534C GLU* 2.8 14.1 + - + +
643C GLN* 4.8 4.0 - - + -
644C THR* 3.1 20.8 + - + +
646C SER* 1.3 75.5 - - - +
648C VAL* 1.3 64.2 + - - +
650C ARG* 3.9 16.1 - - - +
651C GLU* 2.8 34.5 + - + +
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Residues in contact with VAL 648 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643C GLN* 3.1 31.4 - - + +
644C THR 2.9 11.8 + - - +
645C ILE* 2.2 42.6 - - - +
647C ALA* 1.3 82.3 - - - +
649C HIS* 1.3 72.7 + - + +
651C GLU* 3.2 8.5 + - - +
652C SER* 2.9 25.4 + - - -
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Residues in contact with HIS 649 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C TYR* 2.5 27.5 - + - +
266C LEU* 2.4 48.0 - - + +
269C LYS* 5.7 6.7 - - - -
645C ILE* 2.4 69.4 + - + +
646C SER* 4.0 2.7 - - - +
648C VAL* 1.3 77.1 - - + +
650C ARG* 1.3 68.3 + - - +
651C GLU 2.9 1.3 - - - -
652C SER* 2.6 23.5 + - - -
653C LEU* 2.9 11.6 + - - +
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Residues in contact with ARG 650 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479C TYR* 5.0 8.5 - - + +
524C GLU* 3.1 54.2 + - + +
525C LYS 5.6 1.2 - - - -
526C PRO* 5.7 2.2 - - - +
530C LEU* 5.4 11.0 - - + +
531C SER* 5.3 8.3 - - - +
646C SER 2.8 20.2 + - - +
647C ALA* 3.9 14.2 + - - +
649C HIS* 1.3 76.5 - - - +
651C GLU* 1.3 75.7 + - - +
653C LEU* 3.6 7.8 - - + +
654C ASN* 2.9 31.0 + - + +
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Residues in contact with GLU 651 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647C ALA* 2.8 22.4 - - + +
648C VAL* 3.3 9.4 - - - +
649C HIS 2.9 0.4 - - - -
650C ARG* 1.3 99.7 + - + +
652C SER* 1.3 60.7 + - - +
654C ASN* 2.4 52.8 - - - +
655C LYS* 2.8 32.9 + - + +
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Residues in contact with SER 652 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C TYR* 2.4 46.0 - - - -
648C VAL* 2.9 12.9 + - - -
649C HIS* 2.6 10.7 + - - -
651C GLU* 1.3 74.8 - - - +
653C LEU* 1.3 58.5 + - - +
655C LYS* 3.2 8.7 + - - +
656C LEU* 2.8 33.4 + - - +
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Residues in contact with LEU 653 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C TYR* 3.8 24.5 - - + +
479C TYR* 4.3 19.5 - - + -
480C THR* 3.7 31.4 - - + +
483C ARG* 3.3 50.1 + - - +
649C HIS 3.4 12.3 - - - +
650C ARG* 3.6 6.1 - - - +
652C SER* 1.3 79.4 + - - +
654C ASN* 1.3 66.5 + - - +
656C LEU* 3.1 18.1 + - + +
657C MET* 3.0 23.9 + - - +
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Residues in contact with ASN 654 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483C ARG* 6.1 0.4 - - - +
650C ARG* 2.9 13.1 + - + +
651C GLU* 2.4 49.9 - - - +
653C LEU* 1.3 77.7 - - - +
655C LYS* 1.3 115.4 + - - +
657C MET* 3.4 7.8 + - - +
658C LYS* 3.1 24.7 + - - +
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Residues in contact with LYS 655 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651C GLU* 2.8 42.2 + - + +
652C SER* 3.4 10.8 - - - +
654C ASN* 1.3 127.2 + - - +
656C LEU* 1.3 56.0 + - + +
658C LYS* 3.3 10.7 + - + +
659C ASN* 2.3 41.2 + - - +
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Residues in contact with LEU 656 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C GLY 6.6 0.2 - - - -
246C PHE* 4.3 38.8 - - + -
263C GLU* 5.3 8.7 - - + -
264C THR 6.4 0.2 - - - -
265C TYR* 5.1 15.3 - - + -
459C LEU* 4.9 12.8 - - + -
461C ILE* 5.6 6.3 - - + -
483C ARG* 5.3 6.1 - - - +
652C SER* 2.8 16.3 + - - +
653C LEU* 3.1 27.5 + - + +
655C LYS* 1.3 77.8 - - - +
657C MET* 1.3 63.3 + - - +
659C ASN* 3.0 25.8 + - + +
660C LEU* 3.0 17.7 + - + +
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Residues in contact with MET 657 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483C ARG* 4.3 36.5 - - + +
486C GLN* 4.8 12.8 - - - +
487C PHE* 4.5 27.3 - - + -
490C HIS* 6.2 2.7 - - + +
653C LEU 3.0 15.8 + - - +
654C ASN* 3.7 8.1 - - - +
656C LEU* 1.3 77.2 - - - +
658C LYS* 1.3 61.8 + - - +
660C LEU* 3.1 9.8 + - - +
661C TYR* 3.1 24.2 + - + +
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Residues in contact with LYS 658 (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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654C ASN* 3.1 19.6 + - - +
655C LYS* 3.5 12.6 - - + +
656C LEU 3.2 0.2 - - - -
657C MET* 1.3 77.9 - - - +
659C ASN* 1.3 63.8 + - - +
660C LEU 3.5 0.3 + - - -
661C TYR* 3.7 15.7 + - - +
662C SER* 4.0 8.1 + - - -
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Residues in contact with ASN 659 (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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246C PHE* 5.5 11.0 - - + -
248C ARG* 5.4 1.2 + - - -
455C TYR* 4.4 7.6 + - - +
655C LYS* 2.3 36.9 + - - +
656C LEU* 3.0 19.9 + - + +
658C LYS* 1.3 78.7 - - - +
660C LEU* 1.3 60.6 + - + +
662C SER* 2.8 23.4 + - - -
663C THR* 3.7 6.4 - - - +
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Residues in contact with LEU 660 (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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171C SER* 4.3 21.1 - - - +
173C LEU* 3.5 28.9 - - + -
246C PHE* 4.1 16.4 - - + -
459C LEU* 3.1 36.8 - - + -
483C ARG* 5.3 7.9 - - - +
487C PHE* 4.4 17.0 - - + -
656C LEU* 3.0 14.0 + - + +
657C MET* 3.1 15.7 + - - +
659C ASN* 1.3 74.4 - - - +
661C TYR* 1.3 56.4 + - - +
662C SER 3.0 4.9 - - - -
663C THR* 2.2 41.4 + - + +
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Residues in contact with TYR 661 (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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487C PHE* 4.1 21.3 - + + -
490C HIS* 4.1 29.0 + + - -
495C LEU* 4.9 15.0 - - + +
657C MET* 3.1 12.7 + - + +
658C LYS* 3.9 9.2 - - - +
659C ASN 3.6 0.2 - - - -
660C LEU* 1.3 78.2 - - - +
662C SER* 1.3 60.8 + - - +
663C THR 2.8 13.0 + - - +
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Residues in contact with SER 662 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168C GLU* 5.6 1.6 - - - +
169C ASN* 4.5 15.2 + - - +
455C TYR* 4.5 6.1 + - - -
658C LYS 4.0 6.8 + - - -
659C ASN* 2.8 24.5 + - - -
660C LEU 2.9 0.2 + - - -
661C TYR* 1.3 81.3 - - - +
663C THR* 1.3 62.0 + - - +
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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