Contacts of the helix formed by residues 425 - 435 (chain C) in PDB entry 5C51
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 LEU 425 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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422C GLN* 5.7 7.4 - - - +
424C SER* 1.3 81.0 + - - +
426C GLU* 1.3 87.7 + - - +
427C GLN 3.5 0.2 - - - -
428C LEU* 3.5 12.1 - - + +
429C TYR* 2.9 57.6 + - + +
442C LEU* 4.2 23.6 - - + -
463C LYS* 3.5 26.0 - - - +
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Residues in contact with GLU 426 (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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424C SER* 3.3 8.4 + - - +
425C LEU* 1.3 103.8 + - - +
427C GLN* 1.3 59.8 + - - +
429C TYR* 3.4 7.9 + - - +
430C SER* 2.9 27.8 + - - -
463C LYS* 5.0 4.3 - - - -
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Residues in contact with GLN 427 (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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76C ARG* 5.2 1.6 + - - -
421C MET* 5.5 1.0 - - - +
423C SER* 2.6 28.9 + - - +
424C SER* 3.6 22.6 + - - +
426C GLU* 1.3 76.7 - - - +
428C LEU* 1.3 63.3 + - - +
430C SER* 3.6 8.6 - - - -
431C LYS* 2.9 28.1 + - - +
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Residues in contact with LEU 428 (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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386C ASP* 3.7 25.6 - - + +
422C GLN* 5.1 15.0 - - + +
424C SER 3.5 19.5 - - - +
425C LEU* 3.5 15.7 + - + +
427C GLN* 1.3 80.8 - - + +
429C TYR* 1.3 69.4 + - + +
431C LYS* 3.2 22.6 + - - +
432C TYR* 2.9 68.7 + - + +
442C LEU* 5.9 4.3 - - + -
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Residues in contact with TYR 429 (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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425C LEU* 2.9 42.4 + - + +
426C GLU* 3.8 8.3 - - - +
428C LEU* 1.3 85.2 - - + +
430C SER* 1.3 59.6 + - - +
432C TYR* 3.7 5.1 - + - +
433C ASP* 2.9 36.8 + - - +
440C THR* 3.2 32.9 + - + -
441C VAL 6.5 0.2 - - - -
442C LEU* 5.0 13.1 - - + +
454C HIS* 5.0 4.0 + - - +
456C ARG* 3.4 51.1 - - + +
463C LYS* 3.2 35.2 + - - -
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Residues in contact with SER 430 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C ARG* 5.3 2.3 + - - -
370C LYS* 4.6 6.0 + - - +
426C GLU 2.9 19.0 + - - -
427C GLN* 3.6 10.8 - - - -
429C TYR* 1.3 76.1 - - - +
431C LYS* 1.3 57.8 + - - +
433C ASP* 3.2 5.5 + - - +
434C GLU* 2.9 49.7 + - - +
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Residues in contact with LYS 431 (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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76C ARG* 3.3 39.9 - - - +
414C TRP* 5.1 6.9 - - - +
416C GLY* 6.3 0.2 - - - -
427C GLN 2.9 17.8 + - - +
428C LEU* 3.5 22.4 - - - +
430C SER* 1.3 76.4 - - - +
432C TYR* 1.3 81.5 + - - +
434C GLU* 3.4 2.3 + - - +
435C MET* 3.2 51.1 + - + +
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Residues in contact with TYR 432 (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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384C ALA* 4.1 15.3 - - + -
386C ASP* 2.8 37.6 + - - -
414C TRP* 3.6 25.1 + + - -
416C GLY* 3.6 11.8 - - - -
428C LEU* 2.9 45.3 + - + +
429C TYR* 4.0 5.2 - + - +
431C LYS* 1.3 98.9 + - + +
433C ASP* 1.3 62.3 + - - +
435C MET* 3.8 11.2 - - - -
436C SER 3.5 1.7 + - - -
437C ILE* 3.0 37.0 + - + +
440C THR* 3.6 37.5 - - + -
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Residues in contact with ASP 433 (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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370C LYS 4.4 2.2 - - - +
371C VAL* 3.7 32.6 - - + +
372C LEU 3.0 23.9 + - - -
429C TYR 2.9 24.9 + - - +
430C SER* 3.7 6.1 - - - +
431C LYS 3.2 0.2 - - - -
432C TYR* 1.3 80.8 - - - +
434C GLU* 1.3 59.6 + - - +
435C MET 3.1 4.5 - - - -
436C SER* 3.3 8.6 + - - +
437C ILE 4.9 2.5 - - - +
440C THR* 5.1 1.7 - - - +
456C ARG* 3.0 31.3 + - - -
458C ARG* 4.2 14.7 - - - +
461C THR* 4.5 7.1 - - - +
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Residues in contact with GLU 434 (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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72C ILE* 4.2 21.3 - - + +
75C ARG* 3.9 8.4 + - - -
76C ARG* 2.7 55.7 + - + +
78C PHE* 3.6 8.3 - - - -
370C LYS* 3.2 52.0 + - + +
372C LEU* 3.4 26.0 - - - +
430C SER* 2.9 28.2 + - - +
431C LYS 3.4 3.8 + - - +
433C ASP* 1.3 76.1 - - - +
435C MET* 1.3 58.0 + - - +
436C SER 3.4 1.3 - - - -
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Residues in contact with MET 435 (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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199B LEU* 6.1 4.3 - - + -
75C ARG 5.1 0.9 - - - +
76C ARG* 3.9 37.2 - - + +
77C HIS* 5.8 2.2 - - - +
78C PHE* 4.1 14.8 - - - -
102C LEU* 4.5 20.8 - - + +
380C PRO* 4.5 4.3 - - - +
381C ILE* 5.6 1.6 - - - -
414C TRP* 5.1 25.1 - - + -
431C LYS* 3.2 42.7 + - + +
432C TYR* 3.7 13.9 + - - +
433C ASP 3.1 0.6 - - - -
434C GLU* 1.3 78.8 - - - +
436C SER* 1.3 70.6 + - - +
437C ILE* 3.3 23.7 + - + +
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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