Contacts of the helix formed by residues 493 - 509 (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 PRO 493 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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435A ILE* 3.2 19.4 - - + +
438A LEU* 3.6 39.5 - - + -
439A ALA 4.2 3.8 - - - +
442A ALA* 5.8 0.9 - - + -
491A PHE 3.2 9.6 - - - +
492A ALA* 1.3 79.7 - - - +
494A VAL* 1.3 64.2 + - - +
495A ASP 3.3 2.7 - - - -
496A ALA* 3.1 22.3 + - + -
497A VAL 3.3 8.7 + - - -
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Residues in contact with VAL 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A PHE* 3.6 11.5 - - + -
435A ILE* 3.3 9.2 - - + +
492A ALA* 3.0 27.0 + - + +
493A PRO* 1.3 70.6 - - - +
495A ASP* 1.3 59.4 + - - +
496A ALA 3.2 0.5 + - - -
497A VAL* 3.3 3.8 + - - +
498A ALA* 2.9 28.1 + - + +
462B MET* 3.5 18.2 - - + -
477B PHE* 3.5 34.5 - - + -
478B MET* 4.3 19.5 - - + -
481B VAL* 4.3 14.6 - - + -
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Residues in contact with ASP 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A PRO 3.3 1.0 - - - -
494A VAL* 1.3 78.9 - - - +
496A ALA* 1.3 56.4 + - - +
498A ALA* 3.3 6.7 - - - +
499A ASP* 3.0 33.3 + - - +
462B MET* 3.7 7.1 - - - +
463B GLY* 2.8 40.9 + - - +
464B ALA* 3.8 5.6 - - + +
467B SER* 4.2 8.3 + - - -
474B ARG* 2.6 37.4 + - - -
478B MET* 5.3 3.0 - - - +
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Residues in contact with ALA 496 (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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438A LEU* 5.3 5.2 - - + -
493A PRO* 3.1 23.7 + - + +
495A ASP* 1.3 76.4 - - - +
497A VAL* 1.3 61.5 + - + +
499A ASP* 3.2 9.2 + - - +
500A GLN* 2.9 31.7 + - + +
464B ALA* 6.2 0.4 - - - -
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Residues in contact with VAL 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A PHE* 3.8 30.7 - - + +
434A ALA* 3.8 23.8 - - + -
435A ILE* 3.9 31.0 - - + +
438A LEU* 4.0 17.3 - - + -
493A PRO 3.3 10.5 + - - +
494A VAL 3.3 6.8 + - - +
496A ALA* 1.3 72.2 - - - +
498A ALA* 1.3 61.8 + - - +
500A GLN* 3.0 10.5 + - + +
501A ARG* 2.8 37.7 + - + +
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Residues in contact with ALA 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A PHE* 4.2 13.0 - - + -
494A VAL 2.9 14.2 + - - +
495A ASP* 3.3 12.6 - - - +
497A VAL* 1.3 78.1 - - - +
499A ASP* 1.3 58.2 + - - +
501A ARG* 3.3 3.0 + - - +
502A ALA* 2.9 27.4 + - - +
557A ARG* 4.9 1.6 - - - -
458B PHE* 4.3 14.8 - - + -
459B MET* 4.8 1.0 - - + +
462B MET* 3.9 35.4 - - + +
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Residues in contact with ASP 499 (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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495A ASP 3.0 14.6 + - - +
496A ALA* 3.5 10.0 - - - +
497A VAL 3.2 0.2 - - - -
498A ALA* 1.3 77.7 - - - +
500A GLN* 1.3 57.9 + - - +
502A ALA* 3.1 6.0 + - - +
503A LYS* 2.8 29.5 + - - +
557A ARG* 2.8 37.9 + - - -
558A LEU 3.9 5.8 - - - +
559A VAL* 3.5 27.8 - - + +
560A GLY 5.2 1.5 + - - +
463B GLY* 3.6 1.3 - - - -
464B ALA* 2.8 36.1 + - - +
465B GLN* 5.3 0.9 + - - +
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Residues in contact with GLN 500 (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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434A ALA* 6.5 0.2 - - + -
496A ALA* 2.9 19.0 + - + +
497A VAL* 3.0 14.5 + - + +
499A ASP* 1.3 76.5 - - - +
501A ARG* 1.3 63.5 + - + +
503A LYS* 3.0 25.6 + - - +
504A ASP* 2.9 32.8 + - - +
559A VAL* 5.3 2.8 - - - +
560A GLY 5.4 0.8 + - - -
561A GLU* 3.5 36.2 + - - +
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Residues in contact with ARG 501 (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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425A ARG 3.1 23.4 + - - -
426A ASN* 2.8 32.5 + - - +
430A ASP* 4.0 23.3 + - - +
431A PHE* 3.6 32.3 - - - +
434A ALA* 6.1 1.9 - - + +
497A VAL* 2.8 25.7 + - + +
498A ALA 3.8 4.0 - - - +
500A GLN* 1.3 73.6 - - + +
502A ALA* 1.3 57.2 + - - +
504A ASP* 3.3 10.2 + - - +
505A PHE* 2.9 28.8 + - - +
454B LEU* 3.7 11.2 - - - +
458B PHE* 4.5 11.9 - - + -
459B MET* 4.9 1.6 - - - -
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Residues in contact with ALA 502 (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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498A ALA 2.9 14.2 + - - +
499A ASP 3.2 9.4 - - - +
500A GLN 3.1 0.2 - - - -
501A ARG* 1.3 78.3 - - - +
503A LYS* 1.3 57.3 + - - +
505A PHE* 3.2 3.8 + - - +
506A ILE* 3.0 31.9 + - - +
557A ARG* 3.8 36.1 - - + +
459B MET* 3.7 25.1 - - + -
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Residues in contact with LYS 503 (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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499A ASP 2.8 12.7 + - - +
500A GLN* 3.0 28.6 + - - +
502A ALA* 1.3 77.6 - - - +
504A ASP* 1.3 66.0 + - - +
506A ILE* 3.3 8.9 + - - +
507A HIS* 3.0 27.1 + - + +
557A ARG* 4.9 1.5 - - - +
559A VAL* 4.7 5.6 - - + -
561A GLU* 2.8 33.3 + - - +
568A TYR* 3.6 48.4 + - + -
582A PRO* 5.2 9.1 - - + +
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Residues in contact with ASP 504 (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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500A GLN* 2.9 29.5 + - - +
501A ARG* 3.7 12.2 - - - +
503A LYS* 1.3 84.8 + - - +
505A PHE* 1.3 59.9 + - - +
507A HIS* 3.4 9.9 + - - +
508A ASP* 2.9 39.0 + - - +
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Residues in contact with PHE 505 (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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316A GLN* 3.8 28.9 - - + -
317A GLU* 4.9 5.4 - - + -
320A GLY* 4.2 6.1 - - - +
321A SER* 3.4 34.1 - - - -
322A MET* 3.6 17.0 - - - -
501A ARG 2.9 18.0 + - - +
502A ALA* 3.2 7.2 + - - +
504A ASP* 1.3 76.3 - - - +
506A ILE* 1.3 57.9 + - + +
508A ASP* 3.4 7.5 - - + +
509A SER* 2.7 57.4 + - - -
554A GLY* 5.0 12.3 - - - -
459B MET* 4.0 25.4 - - + -
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Residues in contact with ILE 506 (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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502A ALA 3.0 13.4 + - - +
503A LYS* 3.6 9.2 - - - +
505A PHE* 1.3 85.5 - - + +
507A HIS* 1.3 59.5 + - - +
509A SER* 3.4 3.4 + - - -
554A GLY 4.8 5.6 - - - +
555A ILE 4.0 1.8 - - - +
556A ALA* 3.3 28.3 - - - +
557A ARG* 3.3 15.9 - - + +
568A TYR* 3.2 33.2 - - + +
569A TYR 3.5 28.3 - - - +
570A THR* 3.1 19.1 - - + +
573A ASN* 2.8 23.7 + - - -
583A LYS 6.4 0.2 - - - +
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Residues in contact with HIS 507 (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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503A LYS* 3.0 17.5 + - + +
504A ASP* 3.8 11.4 + - - +
506A ILE* 1.3 79.2 - - - +
508A ASP* 1.3 60.7 + - - +
509A SER 3.6 1.2 + - - +
568A TYR* 6.5 0.4 - - + -
573A ASN* 3.8 17.9 + - - +
578A HIS* 3.3 46.8 + + + -
580A GLU 3.1 25.0 + - - -
581A GLU* 4.1 1.8 - - - -
582A PRO* 3.5 50.9 - - + +
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Residues in contact with ASP 508 (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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322A MET* 3.8 39.6 - - + +
504A ASP* 2.9 26.9 + - - +
505A PHE* 3.4 9.4 - - - +
507A HIS* 1.3 78.5 - - - +
509A SER* 1.3 63.1 + - - +
510A LEU* 3.7 2.8 + - - +
577A TYR* 3.5 22.9 + - - -
578A HIS* 2.6 38.0 + - - -
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Residues in contact with SER 509 (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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316A GLN* 3.5 19.0 + - - -
322A MET* 5.7 1.1 - - - -
505A PHE* 2.7 51.5 + - - -
506A ILE* 3.6 10.6 - - - -
507A HIS 3.4 1.9 - - - +
508A ASP* 1.3 78.4 - - - +
510A LEU* 1.3 61.2 + - - +
554A GLY 5.0 1.8 + - - -
570A THR* 3.6 16.0 - - - +
573A ASN* 3.0 25.3 + - - +
574A SER 4.8 1.7 - - - +
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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