Contacts of the helix formed by residues 503 - 508 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380D GLU* 4.5 7.9 - - + -
383D THR* 4.6 7.2 - - + -
384D LEU* 5.4 1.8 - - + -
460D TYR* 3.9 33.6 - - + +
461D GLN 4.4 12.8 + - - +
463D LEU* 3.7 22.9 - - + +
466D TYR* 4.3 26.7 - - + -
502D GLU* 1.3 74.7 - - - +
504D TYR* 1.3 64.7 + - - +
507D LEU* 2.9 43.6 + - + +
521D THR* 4.6 3.1 - - + -
525D LEU* 3.4 34.5 - - + -
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Residues in contact with TYR 504 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182D LEU* 4.5 10.1 - - + -
383D THR* 4.1 28.7 - - + +
384D LEU* 5.2 2.7 - - - -
386D HIS* 4.0 29.2 + - + +
388D HIS* 5.0 2.8 + - - +
389D PRO* 5.7 0.3 - - - +
440D VAL* 5.4 0.2 - - - +
448D ALA* 3.6 40.2 - - + +
451D SER* 3.4 24.9 + - - +
452D ILE* 3.6 22.9 - - + -
455D SER* 4.8 10.3 - - - +
460D TYR* 6.0 0.4 - - - -
502D GLU* 4.5 1.7 - - + +
503D LEU* 1.3 80.3 - - - +
505D PRO* 1.3 71.1 - - + +
507D LEU* 3.2 23.0 - - + +
508D LEU* 3.7 27.0 + - + +
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Residues in contact with PRO 505 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177D VAL* 4.0 16.2 - - + -
182D LEU* 4.1 14.1 - - + +
452D ILE* 4.2 16.2 - - + -
495D TYR* 4.1 10.8 - - - +
501D MET* 3.4 14.6 - - + -
502D GLU* 3.4 26.9 - - + +
504D TYR* 1.3 100.6 - - + +
506D ALA* 1.3 53.9 + - - +
507D LEU 2.6 16.6 + - - -
508D LEU* 2.7 17.0 + - - +
509D VAL* 3.0 18.0 + - + +
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Residues in contact with ALA 506 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463D LEU* 3.3 33.2 - - + -
481D LEU* 3.3 7.4 - - + +
501D MET* 3.3 18.8 - - + +
502D GLU 2.9 21.7 + - - +
503D LEU 4.0 0.2 - - - -
504D TYR 3.4 0.2 - - - -
505D PRO* 1.3 77.9 - - - +
507D LEU* 1.3 56.2 + - - +
509D VAL* 3.7 8.3 - - - -
510D GLU* 2.9 31.5 - - - +
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Residues in contact with LEU 507 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383D THR* 5.3 0.2 - - + -
384D LEU* 3.8 28.0 - - + +
435D ALA* 3.0 24.6 - - - +
503D LEU* 2.9 44.0 + - + +
504D TYR* 3.2 15.2 + - + +
505D PRO 2.6 5.3 + - - -
506D ALA* 1.3 77.1 - - - +
508D LEU* 1.3 64.1 + - + +
510D GLU* 3.5 8.3 - - - +
521D THR* 3.8 16.2 - - + +
522D MET* 3.2 56.1 - - + +
525D LEU* 5.7 0.2 - - + -
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Residues in contact with LEU 508 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182D LEU* 3.8 19.7 - - + -
386D HIS 4.4 8.3 - - - +
389D PRO* 3.5 30.7 - - + -
434D VAL* 3.5 35.0 - - + +
435D ALA* 3.1 2.9 - - - +
436D GLY 3.1 26.9 + - - -
437D GLY* 3.2 9.2 + - - -
438D ARG 6.1 0.4 - - - +
440D VAL* 4.0 14.6 - - + -
448D ALA* 5.7 0.2 - - + -
504D TYR* 3.8 37.0 - - + +
505D PRO 2.7 8.7 + - - -
507D LEU* 1.3 76.7 - - + +
509D VAL* 1.3 54.8 + - - +
510D GLU 3.3 2.5 - - - -
522D MET* 4.7 5.6 - - + -
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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