Contacts of the helix formed by residues 477 - 493 (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 SER 477 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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471A ARG* 4.5 1.3 - - - -
475A PHE 3.5 4.0 + - - -
476A LEU* 1.3 75.5 - - - +
478A CYS* 1.3 65.3 + - - +
479A SER 3.5 3.1 + - - -
480A GLN* 3.2 30.3 + - - +
481A TYR* 3.0 21.7 + - - +
974A MET* 3.6 17.9 + - - -
975A ASN* 4.1 0.2 + - - -
22J T 3.5 23.7 + - - -
23J G 3.5 19.5 - - - -
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Residues in contact with CYS 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A ARG* 4.5 15.9 - - - +
477A SER* 1.3 71.8 - - - +
479A SER* 1.3 57.7 + - - +
481A TYR* 3.8 1.6 - - - +
482A HIS* 2.8 31.0 + - - +
500A LEU* 3.8 33.1 - - + +
504A ARG* 4.4 11.7 - - - -
23J G 2.8 56.0 + - + +
24J A 5.1 2.2 - - - +
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Residues in contact with SER 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A SER* 3.3 3.1 + - - -
478A CYS* 1.3 77.1 - - - +
480A GLN* 1.3 65.1 + - - +
482A HIS* 3.1 8.3 + - - +
483A LYS* 3.0 36.4 + - - +
21J G 5.8 0.2 - - - -
22J T 3.0 38.2 + - - +
23J G 4.4 4.0 + - - -
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Residues in contact with GLN 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A LEU* 3.8 23.0 - - + +
477A SER* 3.2 21.2 + - - +
478A CYS 3.3 0.2 - - - -
479A SER* 1.3 77.8 - - - +
481A TYR* 1.3 67.3 + - - +
483A LYS* 3.1 35.2 + - - +
484A MET* 3.1 22.3 + - - +
473C ASN 3.6 0.3 - - - +
474C THR* 3.4 28.8 - - - +
475C PHE* 4.4 11.5 - - + -
970C ARG* 4.0 19.9 - - - +
21J G 6.0 0.2 - - - -
22J T 4.2 10.2 + - - +
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Residues in contact with TYR 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A CYS* 3.3 21.7 - - - +
470A ILE* 6.1 0.9 - - + -
471A ARG* 3.9 29.8 - - + -
476A LEU* 4.4 12.3 - - + +
477A SER 3.0 18.4 + - - +
478A CYS 3.8 2.5 - - - +
480A GLN* 1.3 76.7 - - - +
482A HIS* 1.3 59.9 + - - +
484A MET* 3.2 18.6 + - + +
485A TYR* 2.8 34.1 + - + -
497A PHE* 3.3 35.6 - + + +
498A GLN 2.6 29.2 + - - -
499A PRO 4.6 2.5 - - - -
500A LEU* 3.6 24.2 - - + -
503A LEU* 3.9 19.7 - - + -
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Residues in contact with HIS 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A CYS 2.8 19.3 + - - +
479A SER* 3.1 8.7 + - - +
481A TYR* 1.3 81.0 - - - +
483A LYS* 1.3 60.0 + - + +
485A TYR* 4.2 16.4 - + - -
486A ARG* 2.9 75.4 + - + +
500A LEU* 4.1 19.1 + - + +
31G G 5.6 7.9 - - + -
32G C 5.6 15.7 + + - -
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Residues in contact with LYS 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A SER* 3.0 22.2 + - - +
480A GLN* 3.1 29.6 + - - +
482A HIS* 1.3 79.6 - - + +
484A MET* 1.3 57.4 + - - +
486A ARG* 3.9 26.0 - - - +
487A THR* 3.0 34.6 + - - -
473C ASN* 2.9 43.8 + - - -
474C THR* 4.5 3.4 - - + -
475C PHE* 4.8 3.4 - - - -
994C TYR* 6.3 0.4 - - - -
1003C MET* 4.3 16.4 - - + -
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Residues in contact with MET 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470A ILE* 5.4 1.3 - - + -
476A LEU* 4.6 13.5 - - + -
480A GLN 3.1 14.2 + - - +
481A TYR* 3.7 26.5 - - + +
483A LYS* 1.3 73.2 - - - +
485A TYR* 1.3 66.9 + - - +
487A THR* 3.4 3.8 + - - -
488A VAL* 3.0 24.3 + - - +
497A PHE* 3.5 40.8 - - + -
470C ILE* 3.6 30.3 - - + -
474C THR* 4.7 6.1 - - + +
476C LEU* 5.2 4.3 - - - -
484C MET* 3.3 33.9 - - - +
497C PHE* 4.4 8.5 - - + -
1003C MET* 5.6 0.7 - - - -
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Residues in contact with TYR 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A TYR* 2.8 31.5 + + + +
482A HIS* 3.7 20.0 - + - +
484A MET* 1.3 79.9 - - - +
486A ARG* 1.3 86.4 + - + +
488A VAL* 3.2 1.7 + - - +
489A LYS* 2.9 50.5 + - + +
495A GLN* 3.4 14.6 + - + -
497A PHE* 3.0 43.0 - - + +
498A GLN 3.5 9.9 - - - -
499A PRO* 3.7 22.9 - - + +
500A LEU 5.8 0.2 - - - -
30G T 3.6 4.0 + - - -
31G G 2.4 34.3 + - - -
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Residues in contact with ARG 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A HIS* 2.9 53.1 + - + +
483A LYS* 3.9 29.9 - - - +
485A TYR* 1.3 87.6 - - + +
487A THR* 1.3 57.8 + - - +
489A LYS* 3.8 4.4 - - - +
490A ALA* 2.9 29.3 + - - +
1003C MET* 4.5 11.2 + - - -
1004C ASN* 5.9 1.0 - - - +
1006C HIS* 3.2 57.7 + - + +
32G C 5.8 2.5 + - - +
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Residues in contact with THR 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A LYS 3.0 20.7 + - - -
484A MET 3.8 3.1 - - - -
485A TYR 3.1 0.2 - - - -
486A ARG* 1.3 78.9 - - - +
488A VAL* 1.3 65.0 + - - +
490A ALA* 3.1 6.3 + - - +
491A ILE* 2.9 34.7 + - + +
466C VAL* 4.4 2.9 - - + -
470C ILE* 3.7 29.6 - - + -
1002C PHE 4.2 15.3 - - - +
1003C MET* 3.4 37.0 + - - +
1005C ALA* 5.6 0.4 - - - -
1006C HIS* 6.0 0.7 - - - +
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Residues in contact with VAL 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A MET 3.0 19.1 + - - +
485A TYR 4.0 2.0 - - - +
487A THR* 1.3 76.0 - - - +
489A LYS* 1.3 58.1 + - - +
492A THR* 2.8 40.9 + - + +
494A ARG 4.8 0.2 - - - +
496A ILE* 3.6 35.9 - - + +
497A PHE* 4.5 12.6 - - + +
462C LEU* 3.7 33.2 - - + -
470C ILE* 3.8 14.6 - - + -
496C ILE* 4.8 4.5 - - + -
497C PHE* 3.8 13.7 - - + -
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Residues in contact with LYS 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A TYR* 2.9 38.4 + - + +
486A ARG* 3.9 4.7 - - - +
488A VAL* 1.3 79.5 - - - +
490A ALA* 1.3 58.0 + - - +
493A GLY* 3.0 30.0 + - - +
494A ARG 3.3 19.7 - - - +
495A GLN* 3.0 34.4 + - + +
496A ILE 5.5 0.2 - - - +
30G T 3.0 11.5 + - - -
31G G 2.3 33.2 + - - +
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Residues in contact with ALA 490 (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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486A ARG 2.9 19.4 + - - +
487A THR* 3.7 4.0 - - - +
489A LYS* 1.3 78.1 - - - +
491A ILE* 1.3 62.4 + - - +
493A GLY* 3.8 5.0 + - - -
1005C ALA* 3.8 13.7 - - + +
1006C HIS* 3.7 35.2 - - + +
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Residues in contact with ILE 491 (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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487A THR* 2.9 15.6 + - + +
488A VAL 4.4 0.9 - - - +
490A ALA* 1.3 77.6 - - - +
492A THR* 1.3 63.9 + - + +
458C ARG 3.2 20.3 - - - +
461C GLY 5.9 0.9 - - - +
462C LEU* 3.9 22.9 - - + -
463C GLN* 4.8 9.9 - - - +
466C VAL* 3.5 38.6 - - + -
1002C PHE* 3.9 30.3 - - + +
1005C ALA* 3.7 18.2 - - + -
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Residues in contact with THR 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A VAL* 2.8 25.6 + - + +
491A ILE* 1.3 79.2 - - + +
493A GLY* 1.3 56.1 + - - +
494A ARG* 2.9 31.4 + - - +
496A ILE* 3.1 25.1 - - + +
458C ARG 4.4 2.9 - - - +
459C GLY* 4.9 2.1 - - - -
460C SER* 3.9 31.6 + - - +
461C GLY 4.7 3.4 - - - +
462C LEU* 3.5 32.5 - - + -
496C ILE* 5.3 1.8 - - + -
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Residues in contact with GLY 493 (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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489A LYS* 3.0 21.2 + - - +
490A ALA 3.8 5.6 + - - -
491A ILE 3.3 3.6 + - - -
492A THR* 1.3 74.5 - - - +
494A ARG* 1.3 58.9 + - - +
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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
------------------------------------------------------------
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