Contacts of the strand formed by residues 437 - 442 (chain B) in PDB entry 5ZOJ
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 TRP 437 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A VAL* 3.7 26.0 - - + -
279B TYR* 3.7 2.9 - - - -
280B TYR* 2.7 80.5 + + + +
282B LEU 2.8 24.7 + - - -
415B ARG* 3.6 28.5 - - + -
416B MET 3.2 15.3 - - - +
417B SER* 3.6 7.4 - - - +
418B PHE* 4.7 2.0 - - - +
431B VAL* 3.2 35.2 + - + -
432B THR* 4.4 4.5 - - + -
434B THR* 3.0 33.7 - - - +
436B CYS* 1.3 75.6 - - - +
438B ILE* 1.3 86.2 + - - +
439B GLU* 4.0 5.4 - - + -
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Residues in contact with ILE 438 (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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277B ILE* 4.0 22.9 - - + -
278B ALA 3.2 7.0 - - - +
279B TYR* 3.8 27.4 - - + -
299B VAL* 4.4 22.4 - - + -
311B PHE* 4.9 0.2 - - + -
336B VAL* 4.6 3.6 - - + -
338B LEU* 4.9 4.7 - - + -
415B ARG* 3.4 1.2 - - - -
416B MET* 2.7 65.9 + - + +
418B PHE* 4.2 24.5 - - + -
437B TRP* 1.3 92.9 - - - +
439B GLU* 1.3 62.1 + - - +
440B LEU* 4.3 1.8 - - + +
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Residues in contact with GLU 439 (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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317A SER* 3.0 32.1 + - - -
319A VAL* 6.0 0.4 - - - -
276B SER 3.7 1.6 - - - +
277B ILE* 3.4 6.6 - - - -
278B ALA* 2.8 41.5 + - + +
280B TYR* 3.8 17.4 + - + -
413B THR* 4.8 8.2 - - - -
414B ILE 3.5 3.1 - - - +
415B ARG* 3.0 41.2 + - + -
437B TRP* 4.0 12.6 - - + -
438B ILE* 1.3 75.6 - - - +
440B LEU* 1.3 63.6 + - - +
441B HIS* 3.7 20.5 + - + -
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Residues in contact with LEU 440 (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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274B TRP* 5.4 1.1 - - + -
275B CYS* 3.5 39.5 - - + -
276B SER 3.7 0.4 - - - +
277B ILE* 3.6 22.0 - - + +
338B LEU* 4.1 11.4 - - + -
345B VAL* 5.0 4.5 - - + -
384B ILE* 4.1 17.3 - - + -
412B CYS 3.6 0.5 - - - +
413B THR* 3.0 11.1 - - - -
414B ILE* 2.4 56.8 + - + +
416B MET* 4.0 25.6 - - + -
438B ILE* 4.3 2.4 - - + +
439B GLU* 1.3 71.2 - - - +
441B HIS* 1.3 63.4 + - - +
442B LEU* 4.8 9.9 - - + -
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Residues in contact with HIS 441 (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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315A LEU* 2.9 35.0 + - + +
317A SER* 3.2 21.6 + - - -
275B CYS* 3.0 8.3 - - - +
276B SER* 2.8 49.5 + - - +
278B ALA* 6.3 1.6 - - + -
412B CYS 3.6 2.0 - - - -
413B THR* 3.6 24.1 - - + +
439B GLU* 3.7 16.9 + - + -
440B LEU* 1.3 77.5 - - - +
442B LEU* 1.3 62.0 + - - +
443B ASN* 3.5 10.8 + - - +
446B LEU* 3.4 23.5 - - + +
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Residues in contact with LEU 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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274B TRP* 3.7 37.7 - - + +
275B CYS* 4.3 4.0 - - + -
340B TYR* 6.1 0.2 - - + -
345B VAL* 4.1 13.5 - - + -
385B PHE* 3.4 46.2 - - + -
412B CYS* 3.0 20.8 + - - +
414B ILE* 3.8 18.4 - - + -
440B LEU* 4.8 8.3 - - + -
441B HIS* 1.3 70.3 - - - +
443B ASN* 1.3 64.5 + - - +
444B GLY 3.3 1.7 + - - -
445B PRO* 3.4 18.9 - - + +
446B LEU* 3.2 25.2 + - - +
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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