Contacts of the strand formed by residues 437 - 441 (chain C) in PDB entry 1U7V
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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A VAL* 3.5 28.0 - - + -
279C TYR* 3.3 6.8 - - - -
280C TYR* 2.8 76.7 + + + +
282C LEU 2.7 32.8 + - - -
415C ARG* 3.8 33.0 - - + -
416C MET 3.0 15.0 - - - +
417C SER* 3.9 5.4 - - - -
418C PHE* 4.7 3.1 - - - -
431C VAL* 3.5 29.8 + - + -
432C THR* 4.6 3.6 - - + -
434C THR* 3.2 26.2 - - - +
436C CYS* 1.3 74.3 - - - +
438C ILE* 1.3 79.9 + - - +
439C GLU* 4.1 7.9 - - + -
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Residues in contact with ILE 438 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C ILE* 3.1 35.7 - - + -
278C ALA 3.0 20.2 - - - +
279C TYR* 3.8 8.1 - - + -
299C VAL* 3.7 20.9 - - + -
311C PHE* 3.4 27.8 - - + -
313C LEU* 4.4 2.5 - - + -
336C VAL* 5.9 0.7 - - + -
338C LEU* 6.2 0.2 - - + -
414C ILE 3.8 0.5 - - - +
415C ARG* 3.5 2.9 - - - -
416C MET* 2.7 56.2 + - + +
418C PHE* 4.5 14.8 - - + -
437C TRP* 1.3 82.3 - - - +
439C GLU* 1.3 58.3 + - - +
440C LEU* 4.3 9.9 - - + -
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Residues in contact with GLU 439 (chain C).
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* 2.7 29.6 + - - -
276C SER 3.7 0.5 - - - +
277C ILE* 3.2 5.9 - - - +
278C ALA* 2.8 47.0 + - + +
280C TYR* 3.5 18.3 + - + -
413C THR* 3.1 27.9 + - + +
414C ILE 3.5 3.4 - - - +
415C ARG* 3.0 31.7 + - + +
437C TRP* 4.1 13.7 - - + -
438C ILE* 1.3 75.9 - - - +
440C LEU* 1.3 63.9 + - - +
441C HIS* 3.6 16.5 + - + -
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Residues in contact with LEU 440 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274C TRP* 5.1 1.3 - - + -
275C CYS* 4.5 12.6 - - - -
276C SER 3.5 2.5 - - - +
277C ILE* 3.5 33.0 - - + -
338C LEU* 3.8 28.3 - - + -
345C VAL* 5.0 5.8 - - + -
384C ILE* 4.6 20.2 - - + -
412C CYS 3.6 0.7 - - - +
413C THR* 3.2 9.5 - - - +
414C ILE* 2.8 50.7 + - + +
416C MET* 4.8 8.3 - - - -
438C ILE* 4.3 11.7 - - + -
439C GLU* 1.3 74.3 - - - +
441C HIS* 1.3 64.4 + - - +
442C LEU* 4.1 9.9 - - + -
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Residues in contact with HIS 441 (chain C).
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* 3.1 34.4 + - + +
316A LEU* 4.7 2.7 - - + -
317A SER* 3.4 28.1 + - - -
275C CYS* 2.9 25.6 - - - -
276C SER* 3.0 28.8 + - - +
412C CYS 3.6 2.7 - - - -
413C THR* 3.4 21.4 + - - -
439C GLU* 3.6 17.3 + - + -
440C LEU* 1.3 75.3 - - - +
442C LEU* 1.3 62.1 + - - +
443C ASN* 3.3 3.7 + - - +
446C LEU* 4.2 17.7 - - + +
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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