Contacts of the helix formed by residues 438 - 446 (chain S) in PDB entry 6CNC
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 ASP 438 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416R ARG 5.0 0.4 + - - -
418R ALA 3.3 24.2 + - - +
419R GLU* 3.0 20.7 - - - +
623R LYS* 5.9 4.1 - - + +
627R TRP* 5.6 5.4 - - - -
435S TRP* 5.7 4.5 - - + -
436S GLY* 3.2 7.1 - - - +
437S THR* 1.3 76.0 - - - +
439S PHE* 1.3 65.5 + - - +
440S ASN* 2.9 17.0 + - - +
441S LEU* 3.2 34.2 + - + +
442S ILE* 3.3 24.5 + - - +
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Residues in contact with PHE 439 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419R GLU* 3.0 20.4 + - + +
429R ILE* 5.5 5.6 - - + -
431R ARG* 4.6 12.3 - - - -
437S THR* 3.2 37.2 - - + -
438S ASP* 1.3 73.7 + - - +
440S ASN* 1.3 67.2 + - - +
441S LEU 3.5 0.2 - - - -
442S ILE* 3.2 9.2 + - + +
443S SER* 2.9 23.1 + - - -
451S ARG* 4.5 14.3 - - - +
454S VAL* 3.4 29.5 - - + +
455S LYS* 3.5 52.7 - - + +
458S PHE* 3.9 25.1 - + + -
47Y C 5.5 3.4 - - - -
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Residues in contact with ASN 440 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419R GLU* 3.0 22.7 + - + +
420R TYR 5.6 2.0 + - - -
421R ASN* 4.9 20.4 - - - +
627R TRP* 5.8 3.8 - - - -
630R LEU* 3.9 13.7 - - - +
631R ASN* 5.2 9.5 + - - +
438S ASP* 2.9 12.9 + - - +
439S PHE* 1.3 75.9 - - - +
441S LEU* 1.3 66.7 + - + +
443S SER* 2.9 19.5 + - - -
444S GLN* 2.9 30.0 + - - +
451S ARG* 5.5 6.1 - - - +
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Residues in contact with LEU 441 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623R LYS* 4.8 10.8 - - + +
626R ILE* 3.9 37.7 - - + -
627R TRP* 5.4 8.7 - - + +
630R LEU* 5.4 1.8 - - + -
431S ALA* 5.8 0.7 - - + -
435S TRP* 3.6 54.7 - - + +
438S ASP* 3.2 32.8 + - + +
439S PHE 3.5 0.2 - - - -
440S ASN* 1.3 84.1 - - + +
442S ILE* 1.3 63.3 + - + +
444S GLN* 3.1 20.8 + - + +
445S LEU* 3.1 17.2 + - - +
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Residues in contact with ILE 442 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428S PHE* 3.6 29.4 - - + +
431S ALA* 3.6 26.2 - - + -
432S LEU* 4.9 11.0 - - + -
436S GLY 4.6 8.3 - - - +
437S THR* 4.9 1.8 - - - +
438S ASP 3.3 23.3 - - - +
439S PHE* 3.2 10.3 + - + +
440S ASN 3.1 0.6 - - - -
441S LEU* 1.3 76.7 - - + +
443S SER* 1.3 63.7 + - - +
445S LEU* 3.0 30.1 + - + +
446S TYR* 3.7 9.1 + - + -
454S VAL* 3.6 35.6 - - + +
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Residues in contact with SER 443 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439S PHE 2.9 11.5 + - - -
440S ASN* 2.9 12.8 + - - -
442S ILE* 1.3 76.3 - - - +
444S GLN* 1.3 64.3 + - - +
446S TYR* 3.1 29.7 + - - +
447S PRO* 3.5 3.8 - - - +
449S ARG 4.5 2.8 + - - -
450S SER 3.9 5.0 + - - -
451S ARG* 3.4 40.8 + - - +
454S VAL* 4.4 7.3 - - - +
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Residues in contact with GLN 444 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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626R ILE* 6.0 1.1 - - + -
630R LEU* 3.3 37.0 - - + +
440S ASN* 2.9 25.6 + - - +
441S LEU* 3.1 14.8 + - + +
443S SER* 1.3 80.8 + - - +
445S LEU* 1.3 65.0 + - + +
447S PRO* 3.2 19.4 - - - +
489S LYS* 5.0 7.3 - - - +
490S LYS* 2.5 50.4 + - - +
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Residues in contact with LEU 445 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427S LYS* 3.7 29.4 - - + +
430S LYS* 5.3 1.6 - - + -
431S ALA* 4.4 17.3 - - + +
435S TRP* 5.0 9.0 - - + -
441S LEU 3.1 12.2 + - - +
442S ILE* 3.0 25.7 + - + +
444S GLN* 1.3 78.5 - - + +
446S TYR* 1.3 77.5 + - + +
447S PRO* 3.5 4.7 - - - +
486S CYS* 3.3 46.9 - - + +
489S LYS* 3.7 24.0 - - + +
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Residues in contact with TYR 446 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420S TRP* 4.5 11.7 - + + -
424S GLU* 2.7 53.2 + - + -
427S LYS* 2.9 39.9 - - + +
428S PHE* 4.4 9.6 - + + -
442S ILE* 4.2 8.7 - - + +
443S SER* 3.1 13.9 + - - +
445S LEU* 1.3 97.9 - - + +
447S PRO* 1.3 60.4 - - - +
448S TYR* 3.0 7.6 - + + +
449S ARG* 2.9 51.1 + - + +
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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