Contacts of the helix formed by residues 642 - 660 (chain B) in PDB entry 1CQT
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 LYS 642 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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628B SER* 5.0 9.7 + - - +
631B ILE* 3.8 18.5 + - - +
632B THR* 3.3 35.2 - - + -
635B ALA* 3.8 7.2 - - + -
641B GLU* 1.3 80.4 - - + +
643B GLU* 1.3 66.8 + - + +
644B VAL 3.7 0.4 - - - -
645B ILE* 3.6 7.3 - - - +
646B ARG* 3.6 31.7 + - - +
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Residues in contact with GLU 643 (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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603B LYS* 3.7 28.2 - - - +
641B GLU* 3.4 19.7 - - - +
642B LYS* 1.3 77.5 - - + +
644B VAL* 1.3 64.4 + - - +
645B ILE 2.8 11.7 + - - -
646B ARG* 3.0 59.1 + - - +
647B VAL* 3.1 34.1 + - - +
710O A 4.4 2.9 + - - +
711O T 4.6 5.4 + - - +
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Residues in contact with VAL 644 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603B LYS* 4.4 8.1 - - - +
606B THR* 3.0 29.6 - - - +
608B ILE* 4.7 13.7 - - + +
640B MET* 4.7 7.4 - - + -
641B GLU* 3.3 33.2 + - + +
643B GLU* 1.3 88.4 - - - +
645B ILE* 1.3 74.8 + - + +
647B VAL* 3.7 4.6 - - - +
648B TRP* 3.4 20.8 + - - +
709O A 4.1 8.1 - - - +
710O A 3.1 18.6 - - - +
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Residues in contact with ILE 645 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608B ILE* 5.3 5.8 - - + -
616B LEU* 4.6 28.3 - - + -
631B ILE* 3.5 39.3 - - + +
634B ILE* 5.1 6.5 - - + +
635B ALA* 4.5 10.5 - - + +
638B LEU* 5.3 4.5 - - + -
640B MET* 4.1 22.0 - - + -
641B GLU 4.1 8.5 - - - +
642B LYS 3.6 9.4 + - - +
643B GLU 2.8 2.0 + - - -
644B VAL* 1.3 98.3 - - + +
646B ARG* 1.3 65.6 + - - +
647B VAL 3.0 2.3 + - - -
648B TRP* 3.4 6.6 + - - +
649B PHE* 3.3 24.7 + - + +
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Residues in contact with ARG 646 (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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631B ILE* 5.2 7.0 - - + -
642B LYS* 3.6 20.9 + - - +
643B GLU* 3.0 67.6 + - - +
645B ILE* 1.3 82.8 - - + +
647B VAL* 1.3 63.6 + - - +
649B PHE* 3.6 7.3 - - - +
650B CYS* 3.1 35.6 + - - +
653B ARG* 4.6 0.3 + - - -
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Residues in contact with VAL 647 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643B GLU* 3.3 33.9 - - - +
644B VAL* 3.7 8.1 - - - +
646B ARG* 1.3 86.7 - - + +
648B TRP* 1.3 67.6 + - - +
649B PHE 3.1 1.3 - - - -
650B CYS* 2.8 9.7 + - + +
651B ASN* 2.8 29.3 + - - +
709O A 4.5 10.8 - - + -
710O A 3.7 35.7 - - + +
711O T 4.6 16.6 - - + -
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Residues in contact with TRP 648 (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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608B ILE* 4.7 8.4 - - + +
613B ARG* 4.6 8.4 - - - +
616B LEU* 3.5 56.9 - - + +
617B GLU* 3.1 24.0 - - - -
619B SER* 5.2 0.4 - - - -
620B PHE* 3.5 43.1 - + + -
644B VAL 3.4 14.3 + - - +
645B ILE* 3.4 8.2 + - + +
647B VAL* 1.3 79.1 - - - +
649B PHE* 1.3 89.0 + + + +
651B ASN* 3.2 3.1 + - - +
652B ARG* 2.8 63.3 + - + +
709O A 2.9 46.1 + - - +
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Residues in contact with PHE 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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616B LEU* 6.3 1.3 - - + -
619B SER* 5.1 7.2 - - - -
620B PHE* 4.1 15.7 - + - -
623B ASN 3.3 22.0 - - - -
624B GLN* 2.9 37.9 - - + -
625B LYS* 4.4 5.2 - - - -
631B ILE* 5.4 12.1 - - + -
634B ILE* 5.2 14.1 - - + -
645B ILE* 3.3 13.0 + - + +
646B ARG* 3.6 11.2 - - - +
647B VAL 3.1 0.2 - - - -
648B TRP* 1.3 101.0 - + - +
650B CYS* 1.3 57.1 + - - +
652B ARG* 3.1 1.0 + - - +
653B ARG* 2.9 59.1 + - - +
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Residues in contact with CYS 650 (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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646B ARG* 3.1 18.8 + - - +
647B VAL* 2.8 12.4 + - + +
649B PHE* 1.3 79.7 - - - +
651B ASN* 1.3 61.7 + - - +
653B ARG* 3.1 27.7 + - - +
654B GLN* 2.9 29.8 + - - +
718P C 5.9 0.4 - - - -
719P T 4.2 30.5 - - + -
720P T 4.8 13.2 - - + +
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Residues in contact with ASN 651 (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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647B VAL* 2.8 25.5 + - - +
648B TRP* 3.5 5.8 - - - +
650B CYS* 1.3 75.6 - - - +
652B ARG* 1.3 62.5 + - - +
654B GLN* 3.4 24.7 + - - +
655B LYS* 3.0 24.7 + - - +
658B ARG* 4.4 4.5 + - - -
708O A 5.5 7.4 - - + +
709O A 3.4 19.0 + - + +
710O A 3.0 45.9 + - - +
711O T 4.1 2.6 + - - +
720P T 5.2 0.5 - - - +
721P A 3.9 6.2 + - - -
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Residues in contact with ARG 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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613B ARG* 2.7 31.9 - - - +
617B GLU* 3.8 20.1 + - - +
620B PHE* 3.4 32.9 - - + -
648B TRP* 2.8 49.5 + - + +
649B PHE 3.6 2.0 - - - +
651B ASN* 1.3 79.3 + - - +
653B ARG* 1.3 61.5 + - - +
655B LYS* 3.3 39.1 - - + +
656B GLU* 3.0 21.5 + - - +
708O A 2.7 41.8 + - - +
709O A 5.3 0.9 - - - -
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Residues in contact with ARG 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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620B PHE* 3.8 9.1 - - + -
624B GLN* 2.9 36.9 + - + +
625B LYS* 4.8 6.7 - - - +
646B ARG 4.6 0.6 + - - -
649B PHE* 2.9 49.0 + - - +
650B CYS* 3.1 38.8 + - - +
652B ARG* 1.3 76.8 - - - +
654B GLN* 1.3 63.2 + - - +
655B LYS 3.1 0.7 + - - -
656B GLU* 3.3 16.3 + - - +
657B LYS* 3.7 18.6 + - - +
719P T 4.4 12.0 + - - -
720P T 5.3 4.8 - - - +
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Residues in contact with GLN 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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650B CYS* 2.9 18.5 + - - +
651B ASN* 3.4 24.4 + - - +
653B ARG* 1.3 78.5 - - - +
655B LYS* 1.3 58.9 + - - +
657B LYS* 3.7 23.0 - - + +
658B ARG* 3.3 25.9 + - - +
806J VAL* 5.0 2.4 - - - +
720P T 3.2 33.9 - - + +
721P A 3.0 28.0 + - + +
722P T 3.4 26.6 + - + +
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Residues in contact with LYS 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 ASN 3.0 17.9 + - - +
652B ARG* 3.3 44.5 - - + +
653B ARG 3.1 0.6 - - - -
654B GLN* 1.3 76.3 - - - +
656B GLU* 1.3 60.6 + - - +
657B LYS 3.0 2.2 - - - -
658B ARG* 2.8 47.0 + - - +
659B ILE* 3.4 19.7 + - + +
804J GLN* 3.6 32.2 - - - +
805J GLY* 4.5 0.9 - - - +
708O A 2.7 28.2 + - + +
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Residues in contact with GLU 656 (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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620B PHE* 4.2 21.7 - - + -
621B LEU* 4.7 9.1 - - - +
624B GLN* 4.1 24.0 + - - +
652B ARG 3.0 13.2 + - - +
653B ARG 3.3 11.4 + - - +
655B LYS* 1.3 76.9 - - - +
657B LYS* 1.3 57.1 + - + +
658B ARG 3.1 0.2 - - - -
659B ILE* 4.7 7.1 - - - +
660B ASN* 2.9 40.5 + - + +
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Residues in contact with LYS 657 (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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653B ARG* 3.8 18.8 - - - +
654B GLN* 3.7 16.8 + - + +
655B LYS 3.0 0.6 - - - -
656B GLU* 1.3 78.6 - - + +
658B ARG* 1.3 58.1 + - + +
660B ASN 3.2 15.8 - - - +
661B PRO* 3.9 13.0 - - - +
720P T 3.2 39.8 + - - -
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Residues in contact with ARG 658 (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 ASN 4.4 3.4 + - - -
654B GLN* 3.3 44.4 + - - +
655B LYS* 2.8 40.6 + - - +
657B LYS* 1.3 83.7 - - + +
659B ILE* 1.3 69.1 + - + +
660B ASN 3.4 1.9 - - - -
661B PRO 5.0 2.4 - - - +
802J PRO* 4.6 7.3 - - - +
803J TYR 5.3 4.0 - - - +
805J GLY* 2.5 43.4 + - - +
806J VAL* 4.0 14.7 - - - +
807J ARG* 5.8 2.7 - - - +
708O A 5.1 3.6 - - - +
722P T 6.0 1.0 - - - +
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Residues in contact with ILE 659 (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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122A GLU* 4.8 9.2 - - - +
655B LYS* 3.4 24.2 + - + +
656B GLU* 4.7 7.6 - - - +
658B ARG* 1.3 83.4 - - + +
660B ASN* 1.3 65.3 + - + +
661B PRO 5.4 0.2 - - - -
802J PRO* 4.3 29.3 - - + +
803J TYR 4.0 5.6 - - - +
804J GLN* 3.5 54.1 - - + +
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Residues in contact with ASN 660 (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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118A LYS* 3.9 32.1 - - + +
121A LEU* 4.6 7.6 - - - +
656B GLU* 2.9 32.7 + - + +
657B LYS* 3.2 11.3 - - - +
659B ILE* 1.3 87.2 - - + +
661B PRO* 1.3 92.7 - - - +
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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