Contacts of the helix formed by residues 588 - 602 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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586A GLU* 2.9 42.5 - - + +
587A ILE* 1.3 75.8 - - - +
589A PRO* 1.3 66.2 - - + +
590A GLN* 3.1 24.9 - - - +
591A GLN* 2.7 51.7 + - - +
592A ALA* 3.1 9.7 + - - -
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Residues in contact with PRO 589 (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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565A LEU* 5.2 6.0 - - + -
587A ILE 4.2 2.7 - - - +
588A TYR* 1.3 86.7 - - + +
590A GLN* 1.3 72.1 + - - +
591A GLN 3.1 4.0 + - - -
592A ALA* 3.4 21.2 + - + +
593A ASP* 3.9 8.5 - - - +
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Residues in contact with GLN 590 (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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588A TYR* 3.0 23.7 + - - +
589A PRO* 1.3 99.2 - - + +
591A GLN* 1.3 63.9 + - + +
593A ASP* 3.9 5.7 - - - +
613A CYS* 3.6 29.6 - - - +
614A ASP* 3.9 20.2 - - - +
618A ASP* 4.5 20.4 - - - +
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Residues in contact with GLN 591 (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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586A GLU 5.0 1.0 - - - +
587A ILE* 4.1 13.6 - - + +
588A TYR* 2.7 42.3 + - + +
590A GLN* 1.3 91.4 - - + +
592A ALA* 1.3 55.3 + - - +
593A ASP* 3.2 3.1 - - - -
594A ALA* 3.0 4.0 + - - +
595A MET* 2.7 34.1 + - - +
613A CYS* 4.3 7.2 - - - -
618A ASP* 3.7 13.2 + - + +
621A SER* 3.1 27.3 + - - -
622A LEU* 3.6 35.9 - - + +
625A THR* 6.2 0.2 - - - -
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Residues in contact with ALA 592 (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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558A LEU* 4.4 3.2 - - + +
565A LEU* 3.5 30.1 - - + -
587A ILE* 4.0 10.3 - - - -
588A TYR 3.1 5.4 + - - +
589A PRO* 3.4 16.7 + - + +
591A GLN* 1.3 75.7 - - - +
593A ASP* 1.3 57.8 + - - +
595A MET* 3.3 2.2 + - - +
596A GLU* 2.8 39.1 + - + +
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Residues in contact with ASP 593 (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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589A PRO 3.9 12.5 - - - +
590A GLN* 3.9 7.9 - - - +
591A GLN 4.4 1.8 - - - -
592A ALA* 1.3 74.9 - - - +
594A ALA* 1.3 75.9 + - - +
596A GLU* 3.2 14.5 + - - +
597A LEU* 3.0 23.0 + - - +
612A PRO* 3.2 43.3 - - + +
613A CYS* 3.4 5.9 + - - -
614A ASP* 5.3 2.1 - - - +
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Residues in contact with ALA 594 (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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591A GLN 3.0 2.1 + - - +
593A ASP* 1.3 83.8 + - - +
595A MET* 1.3 63.7 + - - +
597A LEU* 3.3 2.9 + - - +
598A LEU* 3.1 27.9 + - - +
611A LEU* 3.8 10.0 - - + +
612A PRO* 3.7 21.5 - - + +
613A CYS* 3.6 31.0 - - - -
622A LEU* 3.6 17.0 - - + -
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Residues in contact with MET 595 (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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550A MET* 3.5 32.8 - - + -
558A LEU* 3.9 28.5 - - + -
567A LEU* 3.8 25.6 - - + -
587A ILE* 4.0 20.4 - - + -
591A GLN 2.7 19.4 + - - +
592A ALA* 3.6 9.0 - - - +
594A ALA* 1.3 72.9 - - - +
596A GLU* 1.3 62.9 + - - +
598A LEU* 3.6 3.1 + - + -
599A LEU* 3.2 35.9 + - + +
622A LEU* 4.0 6.4 - - + +
626A LEU* 3.9 17.7 - - + -
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Residues in contact with GLU 596 (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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558A LEU* 3.9 17.2 - - + +
592A ALA* 2.8 22.7 + - - +
593A ASP* 3.4 12.3 + - - +
595A MET* 1.3 74.9 - - - +
597A LEU* 1.3 67.2 + - - +
599A LEU* 3.0 11.8 + - - +
600A GLY* 3.0 19.4 + - - -
464B ALA 4.7 1.0 - - - +
465B GLN* 3.4 40.5 + - + +
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Residues in contact with LEU 597 (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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593A ASP 3.0 13.3 + - - +
594A ALA* 3.5 9.4 - - - +
596A GLU* 1.3 75.1 - - - +
598A LEU* 1.3 54.8 + - - +
600A GLY* 3.0 3.2 + - - -
601A SER* 2.6 48.4 + - - +
606A VAL* 4.8 16.4 - - + -
610A ASP 4.9 7.0 - - - +
611A LEU* 5.1 7.2 - - + -
612A PRO* 4.0 26.5 - - + -
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Residues in contact with LEU 598 (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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548A VAL* 4.3 8.1 - - + -
549A HIS* 4.3 20.4 - - - +
550A MET* 3.7 24.1 + - + +
594A ALA 3.1 17.6 + - - +
595A MET* 3.8 5.8 - - + +
597A LEU* 1.3 80.3 - - + +
599A LEU* 1.3 63.0 + - - +
600A GLY 3.3 0.5 + - - -
601A SER* 3.6 12.6 + - - +
602A TYR* 3.7 10.4 + - - +
606A VAL* 3.5 31.0 - - + -
611A LEU* 4.9 14.4 - - + -
622A LEU* 4.3 11.9 - - + -
623A ALA* 6.0 1.1 - - + -
626A LEU* 3.8 28.9 - - + -
632A LEU* 4.2 11.2 - - + -
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Residues in contact with LEU 599 (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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550A MET* 4.2 16.4 - - + -
553A ASP* 4.2 16.4 - - - +
556A ALA* 4.1 35.2 - - + +
557A ARG* 4.9 0.4 - - - -
558A LEU* 3.7 33.9 - - + +
567A LEU* 4.1 5.2 - - + -
595A MET* 3.2 31.4 + - + +
596A GLU* 3.0 10.8 + - - +
598A LEU* 1.3 78.9 - - - +
600A GLY* 1.3 58.4 + - - +
602A TYR* 4.5 3.5 - - - +
465B GLN* 4.1 23.8 + - - +
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Residues in contact with GLY 600 (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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553A ASP* 5.8 0.2 - - - +
596A GLU 3.0 8.4 + - - -
597A LEU* 3.0 5.3 + - - -
599A LEU* 1.3 76.4 - - - +
601A SER* 1.3 56.2 + - - +
602A TYR* 3.2 15.3 + - - +
465B GLN* 5.1 5.6 - - - +
466B HIS* 6.1 2.9 - - - -
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Residues in contact with SER 601 (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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549A HIS* 5.5 1.4 - - - +
597A LEU* 2.6 31.9 + - - -
598A LEU* 3.6 12.2 + - - +
600A GLY* 1.3 71.5 - - - +
602A TYR* 1.3 54.9 + - - +
604A GLU* 2.7 50.5 + - - +
606A VAL* 4.0 16.6 - - - +
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Residues in contact with TYR 602 (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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196A PRO 3.5 7.3 + - - -
197A SER* 3.4 25.9 - - - -
198A SER* 3.1 24.5 + - - -
199A ARG* 6.0 1.3 - - + -
518A GLU* 4.6 1.0 + - - -
549A HIS* 3.7 17.1 - + - -
550A MET* 3.3 41.1 - - + +
551A LEU 4.1 4.2 + - - -
552A GLN* 3.8 15.4 - - - -
553A ASP* 3.9 40.4 - - + +
598A LEU 3.7 12.2 + - - +
599A LEU 4.5 4.0 - - - +
600A GLY 3.2 8.4 - - - +
601A SER* 1.3 80.3 + - - +
603A PRO* 1.3 81.3 - - + +
604A GLU 3.6 1.3 - - - +
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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