Contacts of the helix formed by residues 640 - 653 (chain A) in PDB entry 3Q6N
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 HIS 640 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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593A VAL 5.1 1.1 - - - -
594A THR* 3.0 31.1 + - - -
595A SER 3.7 1.1 - - - -
596A PRO* 3.6 27.8 - - + +
637A ASN* 3.2 22.4 + - - +
638A PRO 3.5 0.2 - - - -
639A ASP* 1.3 80.0 - - - +
641A SER* 1.3 63.5 + - - +
642A ILE* 2.9 54.7 + - + +
643A ILE* 3.0 6.4 + - + +
644A GLU* 2.8 29.8 + - - +
689B TYR* 5.4 3.1 - - + +
693B LYS* 3.8 24.2 + - - -
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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
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639A ASP 4.0 1.6 + - - -
640A HIS* 1.3 74.4 + - - +
642A ILE* 1.3 62.9 + - - +
644A GLU* 3.8 6.4 - - - +
645A THR* 2.9 28.1 + - - -
693B LYS* 3.6 31.2 + - - +
698B ILE* 4.1 18.1 - - - +
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Residues in contact with ILE 642 (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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596A PRO* 4.5 4.0 - - + -
640A HIS* 2.9 28.1 + - + +
641A SER* 1.3 75.5 + - - +
643A ILE* 1.3 59.8 + - + +
645A THR* 3.4 3.1 + - - -
646A LEU* 2.9 27.4 + - - +
662A LEU* 4.8 2.2 - - + -
666A LEU* 4.0 28.7 - - + -
689B TYR* 3.7 45.5 - - + +
692B ILE* 3.8 25.4 - - + -
693B LYS* 3.8 16.6 - - + -
696B LEU* 4.6 7.5 - - + +
698B ILE* 4.4 6.5 - - + +
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Residues in contact with ILE 643 (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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568A PHE* 3.8 17.1 - - + -
571A LEU* 3.8 11.8 - - + +
575A MET* 5.2 0.9 - - + -
596A PRO* 3.4 37.5 - - + +
597A CYS* 5.0 2.2 - - + -
636A ILE* 4.1 27.1 - - + -
637A ASN 3.5 23.3 - - - +
638A PRO* 4.7 0.2 - - + -
640A HIS* 3.0 4.8 + - + +
642A ILE* 1.3 73.1 - - - +
644A GLU* 1.3 65.1 + - - +
646A LEU* 3.6 14.3 + - + +
647A ARG* 3.1 21.0 + - - +
666A LEU* 4.0 27.1 - - + -
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Residues in contact with GLU 644 (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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567A LYS* 3.1 34.0 + - - +
568A PHE* 4.3 16.1 - - + -
638A PRO 4.5 6.9 + - - +
639A ASP* 6.0 0.9 - - - -
640A HIS 2.8 15.7 + - - +
641A SER* 3.8 7.9 - - - +
643A ILE* 1.3 74.9 - - - +
645A THR* 1.3 64.3 + - - +
647A ARG* 3.2 28.2 + - - +
648A GLN* 3.1 27.4 + - - +
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Residues in contact with THR 645 (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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641A SER* 2.9 18.3 + - - -
642A ILE 3.7 3.6 - - - -
644A GLU* 1.3 71.8 - - - +
646A LEU* 1.3 66.0 + - - +
648A GLN* 3.0 26.4 + - - +
649A LYS* 3.0 39.8 + - + +
696B LEU* 3.8 30.5 - - + -
697B GLY 5.2 2.6 + - - +
698B ILE* 4.0 14.1 - - - +
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Residues in contact with LEU 646 (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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571A LEU* 3.9 9.0 - - + -
575A MET* 4.1 19.7 - - + -
642A ILE 2.9 18.6 + - - +
643A ILE* 3.7 12.8 - - + +
645A THR* 1.3 75.7 - - - +
647A ARG* 1.3 56.9 + - - +
649A LYS* 4.7 4.7 - - + +
650A ALA* 2.9 34.5 + - - +
659A VAL* 4.1 22.7 - - + +
662A LEU* 3.4 26.9 - - + -
663A VAL* 3.9 29.8 - - + -
666A LEU* 4.0 22.9 - - + -
696B LEU* 5.2 0.2 - - - +
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Residues in contact with ARG 647 (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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567A LYS* 3.7 37.6 + - - +
568A PHE* 3.6 29.2 - - + -
571A LEU* 4.0 20.8 - - + +
643A ILE 3.1 14.1 + - - +
644A GLU* 3.3 27.9 + - - +
645A THR 3.2 0.2 - - - -
646A LEU* 1.3 76.8 - - - +
648A GLN* 1.3 75.1 + - - +
650A ALA* 4.0 0.9 - - - +
651A GLU* 3.1 61.4 + - - +
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Residues in contact with GLN 648 (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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644A GLU* 3.1 24.7 + - - +
645A THR* 3.0 25.0 + - - +
647A ARG* 1.3 92.2 + - - +
649A LYS* 1.3 72.1 + - + +
651A GLU* 3.3 4.6 + - - +
652A ALA* 3.0 26.3 + - - +
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Residues in contact with LYS 649 (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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645A THR* 3.0 36.7 + - + +
646A LEU* 4.1 5.6 - - + +
648A GLN* 1.3 79.9 - - - +
650A ALA* 1.3 63.6 + - - +
652A ALA* 3.5 6.3 + - - +
653A ASP* 3.2 23.4 + - - +
656A ASP* 5.4 1.2 - - - +
659A VAL* 3.7 22.9 - - + +
696B LEU* 5.4 9.4 - - + +
697B GLY 5.9 2.2 - - - +
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Residues in contact with ALA 650 (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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571A LEU* 3.7 21.8 - - + -
574A ILE* 4.0 17.0 - - + +
646A LEU 2.9 21.0 + - - +
647A ARG 4.0 1.6 - - - +
649A LYS* 1.3 78.0 - - - +
651A GLU* 1.3 57.4 + - + +
653A ASP 4.1 4.0 - - - -
654A LYS* 3.0 33.8 + - - +
659A VAL* 4.0 20.6 - - + +
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Residues in contact with GLU 651 (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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567A LYS 4.4 3.8 - - - +
570A ASN* 3.3 40.5 + - + +
571A LEU* 4.5 1.4 + - - +
574A ILE* 4.8 8.1 - - + -
647A ARG* 3.1 58.4 + - + +
648A GLN* 4.1 2.5 - - - +
649A LYS 3.3 0.2 - - - -
650A ALA* 1.3 75.1 - - + +
652A ALA* 1.3 68.1 + - - +
653A ASP* 3.0 3.6 + - - -
654A LYS* 4.4 1.8 + - - +
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Residues in contact with ALA 652 (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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648A GLN 3.0 19.3 + - - +
649A LYS* 3.7 6.3 - - - +
651A GLU* 1.3 75.8 - - - +
653A ASP* 1.3 63.1 + - + +
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Residues in contact with ASP 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 LYS 3.2 13.9 + - - +
650A ALA* 3.1 7.2 - - - +
651A GLU 3.0 2.1 - - - -
652A ALA* 1.3 83.0 - - + +
654A LYS* 1.3 63.3 + - - +
655A ASN* 3.1 15.6 + - - +
656A ASP* 3.4 38.8 + - + +
659A VAL* 4.5 1.2 - - - +
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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