Contacts of the strand formed by residues 414 - 419 (chain D) in PDB entry 2R6C
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 ILE 414 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193D LEU* 4.3 19.5 - - + -
219D PHE* 3.7 25.4 - - + -
394D ALA* 4.6 11.4 - - + -
395D PHE 3.3 7.0 - - - +
396D LEU* 3.6 19.7 - - + -
413D GLU* 1.3 70.8 - - - +
415D ILE* 1.3 62.3 - - - +
416D ILE* 3.6 19.2 + - + -
426D THR* 3.6 1.0 - - - -
427D VAL* 2.7 48.4 + - + +
429D LEU* 3.5 39.7 - - + -
438D PHE* 6.0 2.5 - - + -
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Residues in contact with ILE 415 (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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374D ARG 4.8 2.7 - - - +
375D PRO* 3.8 32.1 - - + +
393D VAL 3.6 0.2 - - - +
394D ALA* 3.4 1.4 - - - -
395D PHE* 2.8 49.2 + - + +
397D TYR* 4.5 6.3 - - + -
413D GLU* 4.2 22.7 - - + +
414D ILE* 1.3 72.0 - - - +
416D ILE* 1.3 61.8 + - - +
417D ALA* 3.1 24.0 + - + +
425D GLY* 3.8 9.4 - - - +
426D THR* 4.0 17.9 - - + +
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Residues in contact with ILE 416 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193D LEU* 3.7 27.8 - - + -
196D MET* 4.2 14.8 - - + -
197D THR* 3.8 15.0 - - + -
392D ILE* 4.1 13.5 - - + -
393D VAL 3.9 3.6 - - - +
394D ALA* 4.5 7.4 - - + +
414D ILE* 3.6 13.6 + - + +
415D ILE* 1.3 70.8 - - - +
417D ALA* 1.3 57.2 + - - +
418D LYS 4.0 17.5 - - - +
419D GLN* 4.0 18.4 - - + -
423D PRO 4.5 7.2 - - - +
424D VAL* 3.3 8.0 - - - +
425D GLY 3.1 33.2 + - - +
427D VAL* 4.1 17.3 - - + -
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Residues in contact with ALA 417 (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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376D MET* 5.9 0.9 - - - -
377D MET* 4.0 17.9 - - + +
393D VAL 3.1 7.1 + - - +
395D PHE* 3.7 33.0 - - + -
415D ILE* 3.1 11.8 + - + +
416D ILE* 1.3 72.6 - - - +
418D LYS* 1.3 61.5 + - - +
424D VAL* 3.5 19.9 - - - +
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Residues in contact with LYS 418 (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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377D MET* 4.2 16.2 - - + -
387D GLU* 2.7 32.2 + - + +
388D GLN* 4.1 2.8 - - - +
390D ALA 3.2 16.5 + - - +
391D ASP* 4.6 3.8 - - - +
392D ILE* 2.9 5.8 - - - +
393D VAL* 2.8 46.1 + - + -
416D ILE* 3.5 4.2 - - - +
417D ALA* 1.3 80.3 - - - +
419D GLN* 1.3 67.8 + - - +
420D ARG* 3.3 33.8 - - - +
424D VAL* 4.2 3.6 - - - -
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Residues in contact with GLN 419 (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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196D MET* 2.4 36.6 + - - +
197D THR* 3.5 14.2 - - - +
391D ASP 3.1 8.7 - - - -
392D ILE* 4.0 13.0 - - + +
416D ILE* 4.0 10.1 - - + +
418D LYS* 1.3 79.4 - - - +
420D ARG* 1.3 62.8 + - - +
421D ASN* 2.7 35.0 + - - +
422D GLY 3.6 17.6 - - - +
423D PRO* 2.9 33.5 + - - +
424D VAL* 4.1 7.8 - - - +
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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