Contacts of the helix formed by residues 463 - 474 (chain C) 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 GLN 463 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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491A ILE* 4.8 10.5 - - - +
456C GLN 4.9 4.3 - - - +
457C GLY* 3.0 29.3 + - - +
458C ARG* 4.7 7.9 - - - +
461C GLY 3.5 1.4 + - - -
462C LEU* 1.3 72.7 - - - +
464C PRO* 1.3 64.3 - - + +
465C ALA* 4.1 8.6 - - + +
466C VAL* 2.6 50.6 + - + +
467C CYS 3.2 7.4 + - - -
998C TYR* 4.6 5.7 + - - -
1002C PHE* 4.0 20.4 - - - -
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Residues in contact with PRO 464 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462C LEU 3.5 3.9 - - - +
463C GLN* 1.3 83.7 - - + +
465C ALA* 1.3 56.8 + - + +
467C CYS* 3.4 4.7 + - + +
468C LEU* 2.9 28.8 + - - +
498C GLN* 3.9 19.3 - - + -
502C ALA* 3.7 39.5 - - + +
503C LEU* 3.9 3.9 - - + +
506C ALA* 4.2 10.1 - - + +
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Residues in contact with ALA 465 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463C GLN* 2.8 9.3 + - + +
464C PRO* 1.3 79.7 - - + +
466C VAL* 1.3 58.4 + - - +
468C LEU* 3.4 6.3 + - - +
469C ALA* 2.9 21.1 + - - +
506C ALA* 4.2 11.5 - - + +
510C LEU* 5.4 2.0 - - + -
998C TYR* 3.8 32.8 - - + +
999C LEU* 3.2 16.2 - - + +
1002C PHE* 3.8 10.1 - - + -
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Residues in contact with VAL 466 (chain C).
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* 4.4 4.5 - - + -
491A ILE* 3.5 26.9 - - + -
462C LEU* 4.3 14.4 - - + -
463C GLN* 2.6 39.9 + - + +
465C ALA* 1.3 70.8 - - - +
467C CYS* 1.3 58.8 + - - +
469C ALA* 3.2 2.1 + - + +
470C ILE* 2.9 43.0 + - + +
1002C PHE* 3.4 41.3 - - + -
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Residues in contact with CYS 467 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462C LEU* 3.7 24.0 - - - -
463C GLN 3.2 7.4 + - - -
464C PRO 3.6 2.7 - - - +
466C VAL* 1.3 73.7 - - - +
468C LEU* 1.3 59.7 + - - +
470C ILE* 3.4 8.0 + - - +
471C ARG* 2.9 32.2 + - - +
481C TYR* 3.3 20.5 - - - +
497C PHE* 3.8 10.8 - - + -
498C GLN* 3.3 39.3 - - - -
503C LEU* 3.5 15.2 - - + +
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Residues in contact with LEU 468 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464C PRO 2.9 17.3 + - - +
465C ALA* 3.6 7.2 - - - +
467C CYS* 1.3 75.0 - - - +
469C ALA* 1.3 57.6 + - - +
471C ARG* 4.3 12.6 - - - +
472C VAL* 2.9 49.5 + - + +
503C LEU* 3.6 15.4 - - + +
506C ALA* 4.3 2.5 - - + -
507C GLU* 3.5 50.3 - - + +
510C LEU* 3.7 30.1 - - + -
993C LEU* 4.0 8.3 - - + -
999C LEU* 4.3 3.8 - - + -
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Residues in contact with ALA 469 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465C ALA 2.9 15.7 + - - +
466C VAL* 3.4 12.3 - - - +
468C LEU* 1.3 77.2 - - - +
470C ILE* 1.3 56.4 + - + +
472C VAL* 4.2 1.1 - - - +
473C ASN* 2.8 35.7 + - - +
999C LEU* 3.6 44.2 - - + +
1002C PHE* 4.3 5.2 - - + -
1003C MET* 3.7 10.9 - - + +
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Residues in contact with ILE 470 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484A MET* 3.6 33.2 - - + -
487A THR* 3.7 33.2 - - + -
488A VAL* 3.8 24.9 - - + -
462C LEU* 4.4 2.2 - - + -
466C VAL* 2.9 27.6 + - + +
467C CYS* 3.8 4.0 - - - +
469C ALA* 1.3 74.6 - - - +
471C ARG* 1.3 67.2 + - - +
473C ASN 3.2 0.3 + - - -
474C THR* 2.9 34.8 + - + +
476C LEU* 5.2 3.1 - - + -
481C TYR* 5.9 1.1 - - + -
484C MET* 5.4 1.8 - - + -
497C PHE* 3.9 18.4 - - + -
1003C MET* 4.0 11.7 - - + -
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Residues in contact with ARG 471 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467C CYS 2.9 21.6 + - - +
468C LEU* 4.1 7.4 - - - +
470C ILE* 1.3 75.6 - - - +
472C VAL* 1.3 64.9 + - - +
474C THR* 3.6 4.4 + - - -
475C PHE* 3.1 17.8 + - - -
476C LEU* 3.2 44.6 + - + +
477C SER 4.6 0.9 - - - -
478C CYS* 3.8 29.1 - - - -
481C TYR* 3.7 31.6 - - + +
500C LEU* 4.4 7.2 + - - +
503C LEU* 3.9 29.1 - - + +
504C ARG* 5.3 1.0 - - - +
507C GLU* 3.4 22.6 + - - -
989C LYS* 5.6 0.4 - - - +
990C HIS* 3.8 27.0 + - - -
23L G 4.8 2.2 + - - -
24L A 5.9 0.4 + - - -
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Residues in contact with VAL 472 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468C LEU* 2.9 46.4 + - + +
469C ALA* 4.2 2.2 - - - +
471C ARG* 1.3 78.4 - - - +
473C ASN* 1.3 64.8 + - + +
474C THR 3.3 0.5 + - - -
475C PHE* 3.3 21.0 + - - -
507C GLU* 5.4 0.2 - - - +
971C PHE* 4.6 3.3 - - + -
990C HIS* 4.1 30.2 - - + +
993C LEU* 4.2 19.3 - - + +
994C TYR* 4.0 37.5 - - + +
999C LEU* 5.3 3.1 - - + -
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Residues in contact with ASN 473 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480A GLN* 3.6 0.7 - - - +
483A LYS* 2.9 43.3 + - - -
469C ALA 2.8 22.4 + - - +
470C ILE 4.1 0.9 - - - +
472C VAL* 1.3 79.4 - - + +
474C THR* 1.3 59.2 + - - +
475C PHE* 3.6 9.2 - - - -
650C LEU* 5.7 3.8 - - - +
994C TYR* 3.7 36.1 + - - +
999C LEU* 6.0 3.2 - - - +
1000C GLN* 5.5 7.1 - - - +
1003C MET* 3.9 29.9 - - + +
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Residues in contact with THR 474 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476A LEU* 4.2 12.8 - - + +
480A GLN* 3.4 43.6 - - - +
483A LYS* 4.5 10.3 - - + -
484A MET* 4.7 6.6 - - + +
470C ILE* 2.9 29.5 + - + +
471C ARG 3.6 0.5 + - - -
473C ASN* 1.3 81.4 - - + +
475C PHE* 1.3 73.7 + - - +
476C LEU* 3.2 28.4 + - - +
974C MET* 5.3 0.5 - - - +
1003C MET* 5.4 1.6 - - + -
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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