Contacts of the strand formed by residues 334 - 339 (chain I) in PDB entry 5U07
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 334 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286I ILE 4.2 0.5 - - - +
287I ALA* 3.4 1.7 - - - -
288I VAL* 2.8 43.6 + - + +
290I PHE* 4.6 15.5 - - + -
332I ASP 3.7 13.9 - - - +
333I ALA* 1.3 68.8 - - - +
335I ARG* 1.3 68.0 - - - +
363I MET* 4.7 10.9 - - + +
366I ALA* 5.0 19.1 - - + +
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Residues in contact with ARG 335 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285I HIS* 3.6 24.4 + - - +
286I ILE 3.6 5.6 - - - -
287I ALA* 3.9 13.0 - - + +
289I ARG* 2.8 42.8 - - - +
296I PHE* 5.7 0.6 - - - -
322I ALA* 4.9 8.3 + - - +
325I LEU* 5.3 0.4 - - - +
326I ARG* 2.8 62.6 - - - +
331I ASP* 3.7 5.7 + - - -
333I ALA* 3.3 13.6 + - - +
334I ILE* 1.3 81.0 - - - +
336I GLY* 1.3 58.8 + - - +
348I ALA 3.8 19.4 + - - -
349I LEU* 3.9 9.2 - - - +
350I GLY* 4.4 7.0 - - - +
351I GLU* 4.6 8.0 + - - +
353I TYR* 5.1 1.7 - - - -
363I MET* 3.4 11.5 - - - +
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Residues in contact with GLY 336 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285I HIS* 3.4 4.5 + - - -
286I ILE 2.9 31.1 + - - +
335I ARG* 1.3 79.2 - - - +
337I TYR* 1.3 60.3 + - - -
349I LEU 3.5 9.5 + - - -
351I GLU 3.6 11.4 - - - -
353I TYR* 4.6 0.9 - - - -
359I LEU* 3.6 9.7 - - - +
363I MET* 3.5 12.6 - - - -
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Residues in contact with TYR 337 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283I LEU* 5.0 2.2 - - + -
284I VAL 3.0 14.8 - - - +
285I HIS* 4.1 6.1 - - + -
336I GLY* 1.3 73.9 - - - +
338I ALA* 1.3 69.0 + - - +
339I THR* 4.4 7.9 - - + -
344I THR 5.7 0.7 - - - -
345I ASP* 3.8 13.2 + - - -
346I LEU* 3.4 51.5 + - + -
349I LEU* 3.1 35.0 - - + -
350I GLY 3.2 22.3 + - - -
351I GLU 3.7 3.6 + - - -
352I ARG* 3.2 46.0 - - + +
353I TYR* 2.9 27.4 + - - +
359I LEU* 3.5 7.4 - - - +
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Residues in contact with ALA 338 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283I LEU* 3.7 1.2 - - - -
284I VAL 2.9 30.9 + - - -
337I TYR* 1.3 77.1 - - - +
339I THR* 1.3 61.1 + - - +
353I TYR 3.4 17.7 - - - +
354I ASP 4.8 0.9 - - - +
355I SER* 4.1 12.1 - - - +
356I TYR* 3.8 28.3 - - + -
359I LEU* 3.5 17.4 - - + +
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Residues in contact with THR 339 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282I ASP 3.2 12.4 + - - -
283I LEU* 4.4 13.9 - - + +
337I TYR* 4.4 10.3 - - + -
338I ALA* 1.3 76.9 - - - +
340I VAL* 1.3 61.7 + - - +
341I GLU* 2.8 53.8 + - + +
344I THR 5.3 2.5 - - - +
346I LEU* 5.3 2.9 - - + -
352I ARG* 3.2 29.0 + - - +
353I TYR 4.6 1.9 + - - +
354I ASP* 4.6 9.9 - - - +
356I TYR* 5.2 3.1 - - - -
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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