Contacts of the strand formed by residues 414 - 419 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B LEU* 4.4 18.8 - - + -
219B PHE* 3.6 35.2 - - + -
394B ALA* 4.7 11.9 - - + -
395B PHE 3.3 6.3 - - - +
396B LEU* 3.6 19.1 - - + -
413B GLU* 1.3 71.4 - - - +
415B ILE* 1.3 62.5 + - - +
416B ILE* 3.5 20.9 + - + -
425B GLY 3.8 0.2 - - - +
426B THR* 4.6 0.4 - - - -
427B VAL* 2.7 46.2 + - + +
429B LEU* 3.6 30.7 - - + -
438B PHE* 5.9 1.3 - - + -
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Residues in contact with ILE 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B ARG 4.8 3.1 - - - +
375B PRO* 3.9 33.0 - - + +
393B VAL 3.6 0.3 - - - +
394B ALA* 3.4 1.0 - - - -
395B PHE* 2.7 50.2 + - + +
397B TYR* 4.7 5.4 - - + -
413B GLU* 4.4 21.5 - - + +
414B ILE* 1.3 70.6 - - - +
416B ILE* 1.3 62.9 + - - +
417B ALA* 3.3 26.3 + - + +
425B GLY* 3.7 9.0 - - - +
426B THR* 3.7 17.9 - - - +
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Residues in contact with ILE 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B LEU* 3.8 26.5 - - + -
196B MET* 4.1 15.0 - - + -
197B THR* 3.9 14.4 - - + -
392B ILE* 4.2 14.4 - - + -
393B VAL 3.8 4.5 - - - +
394B ALA* 4.5 6.5 - - + +
414B ILE* 3.5 14.8 + - + +
415B ILE* 1.3 71.9 - - - +
417B ALA* 1.3 58.8 + - - +
418B LYS 3.8 6.5 + - - +
419B GLN* 4.0 32.1 - - + +
423B PRO 4.7 2.5 - - - +
424B VAL* 3.4 6.1 - - - +
425B GLY 3.0 33.0 + - - +
427B VAL* 4.1 19.3 - - + -
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Residues in contact with ALA 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376B MET* 5.9 1.1 - - - -
377B MET* 4.4 16.8 - - + +
393B VAL 3.1 7.3 + - - +
395B PHE* 3.7 32.3 - - + -
415B ILE* 3.3 12.0 + - + -
416B ILE* 1.3 74.2 - - - +
418B LYS* 1.3 60.6 + - - +
424B VAL* 3.5 20.1 - - - +
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Residues in contact with LYS 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A SER* 5.8 7.3 - - - -
377B MET* 4.2 20.4 - - + -
387B GLU* 2.7 31.9 + - + +
388B GLN* 4.1 3.0 - - - +
390B ALA 3.4 14.0 + - - +
391B ASP* 4.6 3.6 - - - +
392B ILE* 2.9 5.1 - - - +
393B VAL* 2.7 42.5 + - + +
416B ILE* 3.5 3.3 - - - +
417B ALA* 1.3 79.6 - - - +
419B GLN* 1.3 68.0 + - - +
420B ARG* 3.2 38.6 - - - +
424B VAL* 4.5 3.8 - - - -
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Residues in contact with GLN 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B MET* 2.4 36.3 + - - +
197B THR* 3.6 15.8 - - - +
391B ASP 3.1 9.4 - - - -
392B ILE* 4.0 13.1 - - + +
416B ILE* 4.0 11.4 - - + +
418B LYS* 1.3 79.0 - - - +
420B ARG* 1.3 61.5 + - - +
421B ASN* 3.1 29.4 + - - +
422B GLY 3.6 19.5 - - - +
423B PRO* 2.9 36.5 + - - +
424B VAL* 4.2 8.1 - - - +
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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