Contacts of the helix formed by residues 588 - 602 (chain B) in PDB entry 4CCN
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 TYR 588 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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565B LEU* 4.7 0.2 - - - -
586B GLU* 3.5 45.1 + - + +
587B ILE* 1.3 76.3 - - - +
589B PRO* 1.3 65.4 - - + +
590B GLN* 3.0 21.1 - - - +
591B GLN* 2.7 49.2 + - + +
592B ALA 3.1 8.1 + - - -
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Residues in contact with PRO 589 (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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565B LEU* 4.5 8.3 - - + -
587B ILE 3.9 2.9 - - - +
588B TYR* 1.3 89.4 - - + +
590B GLN* 1.3 72.3 + - - +
591B GLN 3.1 4.3 + - - -
592B ALA* 3.5 19.0 + - + +
593B ASP* 4.5 6.6 + - - +
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Residues in contact with GLN 590 (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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588B TYR* 2.9 20.4 + - - +
589B PRO* 1.3 98.1 - - - +
591B GLN* 1.3 62.6 + - + +
593B ASP* 3.6 12.4 - - - +
613B CYS* 3.9 15.4 - - - +
614B ASP* 3.2 29.0 + - + +
618B ASP* 4.2 18.2 - - - +
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Residues in contact with GLN 591 (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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586B GLU 5.2 0.9 - - - +
587B ILE* 3.9 13.0 - - + +
588B TYR* 2.7 38.9 + - + +
590B GLN* 1.3 89.9 - - + +
592B ALA* 1.3 57.3 + - - +
593B ASP* 3.0 6.8 + - - -
594B ALA* 3.1 5.2 + - - +
595B MET* 2.8 27.5 + - - +
613B CYS* 5.1 3.4 - - - -
618B ASP* 3.6 16.7 + - + +
621B SER* 2.8 32.5 + - - -
622B LEU* 3.4 38.7 - - + +
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Residues in contact with ALA 592 (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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558B LEU* 4.3 5.6 - - + +
565B LEU* 3.3 34.5 - - + -
587B ILE* 3.6 10.2 - - - +
588B TYR 3.1 5.0 + - - +
589B PRO* 3.5 11.8 + - + +
591B GLN* 1.3 76.9 - - - +
593B ASP* 1.3 56.6 + - - +
595B MET* 3.6 3.2 - - - +
596B GLU* 2.9 37.4 + - + +
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Residues in contact with ASP 593 (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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589B PRO 4.5 4.7 + - - +
590B GLN* 3.6 11.3 - - - +
591B GLN* 3.3 15.0 - - - +
592B ALA* 1.3 71.1 - - - +
594B ALA* 1.3 80.4 + - - +
596B GLU* 3.3 13.0 + - - +
597B LEU* 3.2 19.8 + - - +
612B PRO* 2.7 34.6 - - + +
613B CYS* 4.0 7.6 - - - -
614B ASP* 5.1 2.3 - - - +
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Residues in contact with ALA 594 (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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591B GLN 3.9 0.4 - - - +
593B ASP* 1.3 80.9 + - - +
595B MET* 1.3 65.8 + - - +
597B LEU* 3.3 3.8 + - - +
598B LEU* 3.0 27.4 + - - +
611B LEU* 4.0 20.2 - - + -
612B PRO* 3.8 13.2 + - + -
613B CYS* 3.8 28.9 - - - -
622B LEU* 3.8 17.3 - - + -
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Residues in contact with MET 595 (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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550B MET* 4.1 10.1 - - - -
558B LEU* 4.0 26.9 - - + -
567B LEU* 3.9 28.0 - - + -
587B ILE* 4.1 19.5 - - + -
591B GLN 2.8 17.1 + - - +
592B ALA* 3.6 9.4 - - - +
594B ALA* 1.3 79.0 - - - +
596B GLU* 1.3 62.9 + - - +
598B LEU* 3.8 17.0 - - + -
599B LEU* 3.2 26.2 + - + +
622B LEU* 3.9 6.0 - - + +
626B LEU* 3.9 27.8 - - + -
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Residues in contact with GLU 596 (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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465A GLN* 3.5 39.8 + - + +
558B LEU* 4.0 17.0 - - + -
592B ALA* 2.9 25.1 + - + +
593B ASP* 3.5 11.8 - - - +
594B ALA 3.2 0.2 - - - -
595B MET* 1.3 76.5 - - - +
597B LEU* 1.3 65.0 + - - +
599B LEU* 3.0 18.8 + - - +
600B GLY* 3.1 9.5 + - - -
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Residues in contact with LEU 597 (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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593B ASP 3.2 10.2 + - - +
594B ALA* 3.4 7.9 - - - +
596B GLU* 1.3 77.9 - - - +
598B LEU* 1.3 52.4 + - + +
600B GLY* 2.9 3.5 + - - -
601B SER* 2.5 58.6 + - - +
606B VAL* 4.1 25.1 - - + -
610B ASP 4.9 1.8 - - - +
611B LEU* 4.6 4.5 - - + -
612B PRO* 3.5 31.0 - - + -
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Residues in contact with LEU 598 (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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548B VAL* 4.5 13.5 - - + +
549B HIS* 4.6 10.3 - - - +
550B MET* 3.7 18.2 + - + +
594B ALA 3.0 19.1 + - - +
595B MET* 3.7 15.0 - - + +
597B LEU* 1.3 76.9 - - - +
599B LEU* 1.3 62.1 + - - +
600B GLY 3.0 1.4 + - - -
601B SER* 3.2 13.5 + - - -
602B TYR* 3.6 8.7 + - - +
606B VAL* 3.3 33.0 - - + -
611B LEU* 4.4 14.1 - - + -
622B LEU* 4.4 10.3 - - + -
623B ALA* 6.2 1.3 - - - -
626B LEU* 3.6 30.1 - - + -
632B LEU* 4.2 10.3 - - + -
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Residues in contact with LEU 599 (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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465A GLN* 3.8 23.8 + - - +
466A HIS* 6.1 0.3 - - - -
550B MET* 3.9 31.9 - - + -
553B ASP* 4.3 13.7 - - - +
556B ALA* 4.2 20.6 - - + +
557B ARG* 4.8 1.3 - - - -
558B LEU* 3.7 39.7 - - + +
567B LEU* 4.2 7.6 - - + -
595B MET* 3.4 18.6 - - + +
596B GLU* 3.0 8.3 + - - +
598B LEU* 1.3 76.2 - - - +
600B GLY* 1.3 57.1 + - - +
602B TYR* 4.7 3.9 + - - +
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Residues in contact with GLY 600 (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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465A GLN* 5.7 2.9 - - - -
466A HIS* 6.1 3.1 - - - -
596B GLU 3.1 7.2 + - - -
597B LEU* 2.9 8.4 + - - -
599B LEU* 1.3 80.5 - - - +
601B SER* 1.3 61.5 + - - +
602B TYR 3.4 4.9 + - - +
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Residues in contact with SER 601 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549B HIS* 5.9 1.3 - - - -
597B LEU* 2.5 47.2 + - - +
598B LEU* 3.2 7.9 + - - -
600B GLY* 1.3 76.8 - - - +
602B TYR* 1.3 56.9 + - - +
604B GLU* 2.7 52.2 + - - +
606B VAL* 5.0 11.1 - - - +
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Residues in contact with TYR 602 (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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196B PRO 3.3 7.6 + - - -
197B SER* 3.3 30.3 - - - -
198B SER* 2.9 27.5 + - - -
199B ARG* 5.6 1.8 - - + -
518B GLU* 4.3 1.6 + - - -
549B HIS* 3.7 22.0 - + - +
550B MET* 3.2 35.2 - - + -
551B LEU 4.0 3.0 + - - -
552B GLN* 3.6 16.6 - - - -
553B ASP* 3.5 44.3 - - + +
598B LEU 3.6 10.0 + - - +
599B LEU 4.9 3.1 - - - +
600B GLY 3.4 5.1 - - - +
601B SER* 1.3 78.3 - - - +
603B PRO* 1.3 73.3 - - + +
604B GLU 3.7 0.9 - - - +
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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