Contacts of the helix formed by residues 503 - 508 (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 LEU 503 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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380C GLU* 4.6 7.9 - - + -
383C THR* 4.7 7.0 - - + -
384C LEU* 5.3 1.8 - - + -
460C TYR* 3.9 33.4 - - + +
461C GLN 4.3 13.0 + - - +
463C LEU* 3.7 21.6 - - + +
466C TYR* 4.3 26.7 - - + -
502C GLU* 1.3 74.7 - - - +
504C TYR* 1.3 65.4 + - - +
506C ALA* 3.9 1.4 - - - +
507C LEU* 3.0 48.2 + - + +
521C THR* 4.5 2.7 - - + -
525C LEU* 3.4 34.8 - - + -
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Residues in contact with TYR 504 (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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182C LEU* 4.6 9.0 - - + -
383C THR* 4.1 26.5 - - + -
384C LEU* 5.3 1.1 - - - -
386C HIS* 4.0 29.3 + - + +
388C HIS* 4.9 2.8 + - - +
389C PRO* 5.6 0.3 - - - +
440C VAL* 5.4 0.2 - - - +
448C ALA* 3.5 27.0 - - + +
451C SER* 3.4 36.4 + - - +
452C ILE* 3.7 24.5 - - + -
455C SER* 4.8 10.3 - - - +
460C TYR* 6.0 0.4 - - - -
502C GLU* 4.4 1.7 - - + +
503C LEU* 1.3 79.2 - - - +
505C PRO* 1.4 73.6 - - + +
507C LEU* 3.1 26.8 - - + +
508C LEU* 3.7 27.2 + - + +
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Residues in contact with PRO 505 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C VAL* 4.0 17.3 - - + -
182C LEU* 4.0 13.5 - - + +
452C ILE* 4.2 16.2 - - + -
495C TYR* 4.1 8.7 - - - +
501C MET* 3.4 15.5 - - + -
502C GLU* 3.5 26.7 - - + +
504C TYR* 1.4 99.9 - - + +
506C ALA* 1.3 54.1 + - - +
507C LEU 2.8 15.6 + - - -
508C LEU* 2.8 16.5 + - - +
509C VAL* 2.9 18.3 + - + +
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Residues in contact with ALA 506 (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 LEU* 3.3 35.0 - - + -
481C LEU* 3.3 6.7 - - + +
501C MET* 3.3 15.0 - - + +
502C GLU 2.9 20.7 + - - +
503C LEU 4.0 0.2 - - - -
505C PRO* 1.3 78.1 - - - +
507C LEU* 1.3 50.3 + - - +
509C VAL* 3.6 11.2 - - - -
510C GLU* 2.8 39.5 - - - +
521C THR* 5.7 0.2 - - - -
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Residues in contact with LEU 507 (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* 5.3 0.2 - - + -
384C LEU* 3.9 26.5 - - + -
435C ALA* 2.9 24.4 - - - +
503C LEU* 3.0 45.7 + - + +
504C TYR* 3.1 17.2 + - + +
505C PRO 2.8 1.4 + - - -
506C ALA* 1.3 79.3 - - - +
508C LEU* 1.3 60.4 + - + +
510C GLU* 3.5 9.3 - - - +
521C THR* 3.9 14.4 - - + +
522C MET* 3.2 59.4 - - + +
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Residues in contact with LEU 508 (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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182C LEU* 3.8 20.0 - - + -
386C HIS 4.4 7.6 - - - +
389C PRO* 3.6 31.2 - - + -
434C VAL* 3.4 36.0 - - + +
435C ALA* 3.2 3.2 - - - +
436C GLY 3.1 26.0 + - - -
437C GLY* 3.1 9.9 + - - -
438C ARG 6.1 0.7 - - - +
440C VAL* 4.0 14.4 - - + -
504C TYR* 3.8 36.6 - - + +
505C PRO 2.8 5.6 + - - +
507C LEU* 1.3 72.5 - - + +
509C VAL* 1.3 58.4 + - - +
510C GLU 3.2 4.7 - - - -
522C MET* 4.8 5.4 - - + -
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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