Contacts of the helix formed by residues 445 - 457 (chain C) in PDB entry 1CX2
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 445 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175C LYS* 3.0 28.0 + - - +
178C LEU* 3.7 6.6 - - + +
179C GLU* 5.2 1.6 - - - +
183C LEU* 3.4 39.4 - - + +
440C VAL* 4.1 9.9 - - - -
441C PRO 3.0 4.2 + - - -
442C ILE* 2.9 34.2 + - - +
443C ALA 2.9 4.5 + - - +
444C VAL* 1.3 78.7 - - - +
446C ALA* 1.3 60.1 + - + +
448C ALA* 3.3 4.0 + - - +
449C LYS* 2.8 33.8 + - - +
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Residues in contact with ALA 446 (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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175C LYS* 5.9 0.7 - - - +
443C ALA 3.7 8.9 + - - +
445C GLN* 1.3 83.8 - - + +
447C VAL* 1.3 61.5 + - + +
449C LYS* 3.2 11.5 - - - +
450C ALA* 3.0 26.5 + - - +
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Residues in contact with VAL 447 (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 HIS* 5.1 0.2 - - + -
388C HIS* 3.1 33.9 - - + +
444C VAL* 3.3 28.3 - - + +
446C ALA* 1.3 77.5 - - + +
448C ALA* 1.3 66.6 + - - +
449C LYS 2.9 0.9 + - - -
450C ALA* 3.0 5.7 + - - +
451C SER* 2.9 28.6 + - - +
682C HEM 3.4 58.8 - - + +
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Residues in contact with ALA 448 (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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178C LEU* 4.6 7.9 - - + -
182C LEU* 5.7 3.8 - - + -
388C HIS* 5.1 2.4 + - + +
440C VAL* 3.5 36.6 - - + -
444C VAL* 3.0 2.1 + - + +
445C GLN* 3.4 9.4 - - - +
447C VAL* 1.3 81.7 - - - +
449C LYS* 1.3 58.9 + - - +
451C SER* 3.5 4.0 - - - -
452C ILE* 3.0 30.3 + - - +
504C TYR* 3.5 22.3 - - + +
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Residues in contact with LYS 449 (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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173C ASP* 6.1 0.4 - - - -
174C SER* 4.4 11.2 - - - -
175C LYS* 3.8 28.5 - - + +
178C LEU* 3.5 27.6 - - + +
445C GLN 2.8 14.5 + - - +
446C ALA* 3.2 15.3 - - - +
448C ALA* 1.3 72.9 - - - +
450C ALA* 1.3 53.8 + - - +
452C ILE* 2.6 29.5 + - - +
453C ASP* 2.5 42.9 + - - +
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Residues in contact with ALA 450 (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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446C ALA 3.0 8.5 + - - +
447C VAL* 3.0 9.2 + - - +
449C LYS* 1.3 77.2 - - - +
451C SER* 1.3 58.1 + - - +
453C ASP* 3.0 8.5 + - - -
454C GLN* 2.6 46.4 + - - +
682C HEM 3.3 24.7 - - + +
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Residues in contact with SER 451 (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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383C THR* 5.5 1.1 - - - -
386C HIS* 3.1 28.1 - - - -
447C VAL* 2.9 15.6 + - - +
448C ALA* 3.5 3.5 - - - -
450C ALA* 1.3 76.4 - - - +
452C ILE* 1.3 62.7 + - - +
454C GLN* 4.3 7.1 - - - +
455C SER* 2.9 32.0 + - - -
504C TYR* 3.4 40.6 + - - -
682C HEM 4.6 1.0 + - - -
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Residues in contact with ILE 452 (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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174C SER* 3.9 26.5 - - - +
177C VAL* 4.5 3.6 - - + -
178C LEU* 4.1 10.8 - - + +
182C LEU* 3.5 26.7 - - + -
448C ALA 3.0 18.2 - - - +
449C LYS* 2.6 13.6 + - - +
451C SER* 1.3 74.9 - - - +
453C ASP* 1.3 60.0 + - - +
454C GLN 3.3 0.5 + - - -
455C SER* 3.6 2.3 + - - -
456C ARG* 2.9 50.7 + - - +
495C TYR* 4.8 1.3 - - - +
502C GLU* 4.0 10.1 - - - +
504C TYR* 3.7 19.7 - - + -
505C PRO* 4.2 12.6 - - + -
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Residues in contact with ASP 453 (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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174C SER* 3.4 21.8 + - - +
449C LYS* 2.5 57.1 + - - +
450C ALA* 3.0 7.0 + - - -
452C ILE* 1.3 72.0 - - - +
454C GLN* 1.3 57.2 + - - +
456C ARG* 3.3 17.3 - - - +
457C GLU* 3.2 21.3 + - - +
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Residues in contact with GLN 454 (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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214C HIS* 5.1 11.4 - - - -
218C PRO* 4.0 31.7 - - + +
386C HIS* 5.5 3.0 + - - -
450C ALA* 2.6 30.6 + - - +
451C SER* 3.9 5.2 - - - +
453C ASP* 1.3 70.0 - - - +
455C SER* 1.3 60.7 + - - +
456C ARG 2.9 4.3 - - - -
457C GLU* 2.8 29.9 + - - +
458C MET* 2.9 17.3 + - + +
682C HEM 3.1 30.2 + - - +
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Residues in contact with SER 455 (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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383C THR* 2.8 31.3 + - - +
451C SER* 2.9 18.4 + - - -
452C ILE 4.0 3.6 - - - -
454C GLN* 1.3 78.6 - - - +
456C ARG* 1.3 56.3 + - - +
458C MET* 3.9 6.2 - - - +
459C LYS 3.8 1.0 + - - -
460C TYR* 3.1 62.2 + - - +
502C GLU* 5.8 1.8 - - - -
504C TYR* 4.8 7.9 - - - +
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Residues in contact with ARG 456 (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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163C MET* 6.3 3.4 - - + -
171C LEU* 4.0 14.8 - - + +
172C PRO 2.8 37.6 + - - -
173C ASP* 4.1 5.1 + - - +
174C SER* 2.9 27.2 + - - +
452C ILE* 2.9 28.6 + - - +
453C ASP* 3.3 18.7 - - - +
454C GLN 2.9 0.2 - - - -
455C SER* 1.3 77.3 - - - +
457C GLU* 1.3 65.4 + - - +
458C MET 3.3 0.2 - - - -
459C LYS* 3.1 21.1 + - - +
460C TYR 4.9 1.8 - - - +
495C TYR* 3.8 8.7 + - - -
502C GLU* 2.8 39.8 + - - +
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Residues in contact with GLU 457 (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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132C VAL* 5.6 0.3 - - - +
218C PRO* 3.5 30.0 - - + +
453C ASP 3.2 10.4 + - - +
454C GLN* 2.8 17.0 + - - +
456C ARG* 1.3 75.9 - - - +
458C MET* 1.3 53.6 + - - +
459C LYS* 2.7 25.9 + - - +
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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
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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