Contacts of the strand formed by residues 441 - 446 (chain B) in PDB entry 2EZ9
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 VAL 441 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389B ILE* 3.3 13.7 - - + +
391B SER 5.3 0.7 - - - +
429B ALA* 3.6 40.8 - - + +
432B ALA* 3.8 26.2 - - + +
433B LYS* 3.8 29.1 - - - +
436B TYR 4.8 1.1 - - - +
439B ARG 3.5 12.1 + - - +
440B GLN* 1.3 81.8 - - - +
442B PHE* 1.3 66.8 + - - +
466B PRO 4.4 1.4 + - - +
467B VAL* 3.7 5.5 - - + -
468B ILE* 2.9 28.1 + - - +
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Residues in contact with PHE 442 (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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380B VAL* 4.0 24.5 - - + -
383B ILE* 4.0 15.3 - - + -
384B ALA* 4.1 10.3 - - + -
388B ALA* 4.0 7.0 - - + -
389B ILE 2.9 10.1 + - - +
390B TYR* 3.4 40.6 - + + -
391B SER* 2.8 33.3 + - - -
440B GLN* 3.2 39.0 - - + -
441B VAL* 1.3 82.4 - - - +
443B ASN* 1.3 56.4 + - - +
444B LEU* 4.0 14.6 - - + -
467B VAL* 4.4 0.4 - - - -
468B ILE* 3.3 38.1 - - + -
470B VAL* 4.6 2.9 - - + -
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Residues in contact with ASN 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B SER 3.3 3.8 - - - -
425B GLY* 3.1 38.1 - - - +
426B ILE* 3.5 20.8 - - - +
429B ALA* 3.8 10.5 - - + -
442B PHE* 1.3 71.0 - - - +
444B LEU* 1.3 59.2 + - - +
445B ALA* 3.7 16.5 - - - +
450B ALA* 5.8 0.6 - - - +
457B LEU* 5.1 0.4 - - - +
467B VAL* 3.9 1.7 - - + +
468B ILE 2.9 8.7 + - - +
469B ASN* 2.9 34.4 + - - +
470B VAL* 2.8 33.2 + - - +
471B VAL* 5.6 4.0 - - - +
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Residues in contact with LEU 444 (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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377B LEU* 4.0 24.7 - - + -
380B VAL* 4.2 13.7 - - + -
390B TYR* 4.0 20.6 - - + -
391B SER 2.9 11.5 + - - +
392B ILE* 3.5 10.3 - - + -
393B ASP 2.9 24.6 + - - -
397B ILE* 3.8 24.0 - - + +
401B ALA* 4.6 1.3 - - + -
405B LEU* 4.2 13.2 - - + -
442B PHE* 4.0 17.5 - - + -
443B ASN* 1.3 78.5 + - - +
445B ALA* 1.3 59.5 + - - +
470B VAL* 3.6 27.8 - - + -
472B PHE* 4.4 4.5 - - + -
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Residues in contact with ALA 445 (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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393B ASP* 3.7 21.8 - - + +
397B ILE* 4.6 1.8 - - - -
425B GLY* 5.0 0.2 - - - -
426B ILE* 5.7 0.4 - - + +
443B ASN* 3.7 19.7 - - - +
444B LEU* 1.3 75.3 - - - +
446B GLY* 1.3 68.3 + - - +
450B ALA* 4.1 15.0 - - + -
470B VAL 3.0 9.8 + - - +
471B VAL* 3.2 6.8 - - + -
472B PHE* 2.9 30.0 + - - -
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Residues in contact with GLY 446 (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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393B ASP* 4.4 4.0 - - - +
394B VAL 5.6 0.4 + - - -
397B ILE* 4.4 12.6 - - - +
445B ALA* 1.3 75.6 - - - +
447B ASP* 1.3 60.8 + - - -
448B GLY 3.3 2.5 - - - -
449B GLY 3.4 0.5 + - - -
450B ALA* 2.9 28.2 + - - +
471B VAL* 4.2 0.7 - - - -
472B PHE* 3.8 11.9 - - - -
1613B TDK 3.6 29.2 + - - -
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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