Contacts of the helix formed by residues 558 - 570 (chain A) in PDB entry 6CIM
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 ARG 558 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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512A PRO* 6.0 0.2 - - - +
517A PHE* 3.6 12.9 - - - -
526A VAL* 3.9 11.4 - - - +
527A SER* 3.5 27.0 + - - +
528A SER 4.7 0.2 - - - -
529A ARG 2.8 30.2 + - - -
532A VAL* 3.4 25.0 - - + +
533A GLY 4.3 6.5 + - - -
535A ILE* 4.6 6.2 - - + +
556A ARG* 4.1 3.1 - - - +
557A PHE* 1.3 74.0 - - - +
559A TYR* 1.3 55.1 + - - +
560A ASP* 2.9 33.2 + - - +
561A SER* 2.9 13.6 + - - -
562A ALA* 2.7 32.2 + - - +
678A GLU* 3.3 27.4 - - + +
169B THR* 4.6 0.2 - - - -
170B GLU* 3.1 39.2 + - + -
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Residues in contact with TYR 559 (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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557A PHE 3.5 1.6 + - - -
558A ARG* 1.3 71.5 - - - +
560A ASP* 1.3 57.0 + - - +
562A ALA* 3.5 1.2 + - - +
563A LEU* 3.0 45.4 + - + +
595A VAL* 4.0 5.6 - - + +
597A GLU* 2.7 43.9 + - + +
622A PHE* 4.3 8.1 - + - -
624A PHE* 4.0 8.7 - + + +
655A LEU* 3.6 35.4 - - + -
675A LEU* 3.6 26.0 - - + -
678A GLU* 3.0 24.1 + - + +
679A ARG* 3.7 11.7 - - + -
682A MET* 3.4 15.7 - - + -
702A PHE* 3.5 17.1 - + - -
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Residues in contact with ASP 560 (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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517A PHE* 3.4 12.5 - - - -
519A TRP* 3.5 32.0 + - + +
523A LEU* 3.9 13.5 - - + +
526A VAL* 4.2 6.1 - - - +
527A SER 4.5 0.7 - - - +
558A ARG* 2.9 46.5 + - - +
559A TYR* 1.3 75.9 - - - +
561A SER* 1.3 72.2 + - - -
563A LEU* 3.0 5.3 + - - +
564A VAL* 2.9 33.8 + - - +
678A GLU* 5.1 1.8 - - + +
682A MET* 3.6 16.6 - - + +
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Residues in contact with SER 561 (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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512A PRO* 3.9 6.9 - - - +
513A GLY* 3.5 13.7 + - - -
517A PHE* 4.3 15.3 - - - -
530A THR 4.5 3.5 + - - -
532A VAL* 3.3 39.9 + - - +
558A ARG* 2.9 11.9 + - - -
560A ASP* 1.3 86.3 + - - +
562A ALA* 1.3 55.0 + - - +
564A VAL* 3.2 6.6 + - - +
565A SER* 2.9 27.0 + - - -
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Residues in contact with ALA 562 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512A PRO* 4.4 7.5 - - - +
557A PHE* 4.0 9.0 - - + -
558A ARG 2.7 17.2 + - - +
559A TYR 3.8 3.8 - - - +
561A SER* 1.3 72.7 - - - +
563A LEU* 1.3 58.2 + - - +
565A SER 3.3 0.8 + - - +
566A ALA* 2.9 29.8 + - - +
624A PHE* 3.7 13.0 - - + -
655A LEU* 3.7 26.0 - - + -
992A TRP* 3.5 18.1 - - + -
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Residues in contact with LEU 563 (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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519A TRP* 5.6 1.1 - - + -
559A TYR* 3.0 41.0 + - + +
560A ASP* 3.0 10.1 + - - +
562A ALA* 1.3 77.1 - - - +
564A VAL* 1.3 61.7 + - + +
566A ALA* 3.4 1.8 + - + +
567A LEU* 3.0 33.1 + - + +
593A VAL* 5.3 0.2 - - + -
595A VAL* 3.9 13.9 - - + -
624A PHE* 3.9 22.7 - - + -
626A VAL* 4.9 6.1 - - + -
682A MET* 3.7 15.7 - - - -
687A LEU* 5.7 0.2 - - + -
700A PHE* 3.7 33.7 - - + -
702A PHE* 3.6 19.3 - - + -
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Residues in contact with VAL 564 (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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515A HIS* 4.4 11.0 - - + +
517A PHE* 3.5 46.9 - - + -
560A ASP 2.9 18.3 + - - +
561A SER* 3.4 7.2 - - - +
563A LEU* 1.3 73.9 - - - +
565A SER* 1.3 66.9 + - - +
567A LEU* 3.3 2.3 + - - +
568A MET* 3.0 28.0 + - + +
687A LEU* 4.0 17.5 - - + -
689A LEU* 3.9 31.6 - - + -
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Residues in contact with SER 565 (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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509A VAL 4.9 1.0 + - - -
510A LEU 3.2 24.8 + - - +
511A LEU 3.4 9.7 + - - -
512A PRO* 3.7 21.8 - - - -
513A GLY 5.3 0.4 - - - -
515A HIS* 5.4 3.6 - - - -
561A SER 2.9 10.6 + - - -
562A ALA 3.3 0.9 + - - -
564A VAL* 1.3 77.5 - - - +
566A ALA* 1.3 63.0 + - - +
568A MET* 3.4 4.7 + - - +
569A ASP* 3.0 23.7 + - - +
992A TRP* 3.4 20.7 + - - -
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Residues in contact with ALA 566 (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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562A ALA 2.9 17.6 + - - +
563A LEU* 3.8 3.8 - - - +
565A SER* 1.3 77.4 - - - +
567A LEU* 1.3 63.3 + - + +
569A ASP* 3.2 10.1 + - - +
570A MET* 3.0 27.9 + - + +
624A PHE* 4.0 14.6 - - + -
626A VAL* 4.6 9.6 - - + -
653A LYS* 3.6 29.2 - - + +
992A TRP* 3.9 4.8 - - - -
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Residues in contact with LEU 567 (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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563A LEU* 3.0 22.4 + - + +
564A VAL 3.8 3.8 - - - +
565A SER 3.3 0.2 - - - -
566A ALA* 1.3 75.0 - - + +
568A MET* 1.3 67.2 + - - +
570A MET* 3.0 12.6 + - + +
571A GLU* 3.0 20.4 + - - +
574A ILE* 4.3 12.1 - - + +
593A VAL* 4.5 12.8 - - + -
626A VAL* 5.2 3.6 - - + -
629A ILE* 3.9 27.8 - - + -
687A LEU* 4.1 7.6 - - + -
689A LEU* 4.4 8.7 - - + -
691A MET* 4.5 3.3 - - - +
698A PHE* 3.9 33.7 - - + -
700A PHE* 3.9 27.1 - - + -
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Residues in contact with MET 568 (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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515A HIS* 3.2 60.6 - - + +
564A VAL 3.0 20.6 + - - +
565A SER* 3.8 3.8 - - - +
567A LEU* 1.3 75.2 - - - +
569A ASP* 1.3 65.4 + - - +
571A GLU* 3.2 31.5 + - - +
689A LEU* 3.8 21.3 - - + -
690A GLU 3.7 17.9 - - - +
691A MET* 3.8 24.2 - - + -
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Residues in contact with ASP 569 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510A LEU* 4.8 10.9 - - + +
565A SER 3.0 14.5 + - - +
566A ALA* 3.3 12.5 - - - +
568A MET* 1.3 78.5 - - - +
570A MET* 1.3 59.7 + - - +
571A GLU 3.3 0.7 + - - -
572A GLU* 4.4 5.0 + - - +
573A ASP* 4.8 2.6 - - - +
653A LYS* 3.5 11.2 + - - +
992A TRP* 6.2 1.1 - - + +
995A THR 4.3 0.2 - - - +
996A SER* 3.1 18.2 - - - -
997A LYS* 2.5 32.1 + - - +
998A TYR* 2.9 45.2 + - - +
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Residues in contact with MET 570 (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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566A ALA* 3.0 17.9 + - + +
567A LEU* 3.0 13.2 + - - +
569A ASP* 1.3 74.2 - - + +
571A GLU* 1.3 65.7 + - - +
572A GLU 3.3 3.1 - - - -
573A ASP* 3.0 17.8 + - + +
574A ILE* 2.9 27.0 + - + +
626A VAL* 3.8 35.2 - - + -
629A ILE* 4.0 15.7 - - - -
641A PHE* 3.5 24.9 - - + -
643A GLU* 5.4 0.2 - - - +
653A LYS* 6.5 0.9 - - + -
997A LYS* 3.5 34.1 - - + -
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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