Contacts of the strand formed by residues 367 - 372 (chain I) in PDB entry 4ZZ7
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 THR 367 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273I PHE* 3.4 8.2 - - - -
305I MET* 4.2 3.4 - - - -
336I ILE* 3.7 29.3 - - + +
346I ILE* 5.6 0.2 - - - -
348I VAL* 3.2 14.6 - - - -
349I ASP* 4.5 0.7 - - - -
350I GLY* 3.2 24.9 - - - +
364I VAL* 4.6 0.9 - - + -
365I GLY 3.1 18.2 - - - +
366I GLY* 1.3 71.9 - - - -
368I LEU* 1.3 59.9 + - - +
369I ILE* 4.2 5.7 - - - +
386I PRO 3.0 8.3 + - - +
387I VAL* 3.5 22.2 - - - +
388I LEU 3.1 21.7 + - - -
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Residues in contact with LEU 368 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298I VAL* 4.1 18.2 - - + +
301I MET* 4.0 17.5 - - + -
302I THR* 3.8 22.7 - - - +
305I MET* 3.6 31.4 - - + -
346I ILE* 3.7 0.9 - - - -
347I VAL* 3.0 30.9 + - + -
348I VAL* 3.0 20.5 + - + +
367I THR* 1.3 72.1 - - - +
369I ILE* 1.3 87.3 + - - +
388I LEU* 3.5 17.0 - - + +
390I VAL* 3.8 18.8 - - + -
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Residues in contact with ILE 369 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335I TYR 5.1 0.2 - - - +
336I ILE* 4.4 13.2 - - + -
339I ALA* 3.7 24.7 - - + -
344I ALA* 3.5 28.7 - - + -
345I THR 3.4 7.2 - - - +
346I ILE* 3.9 16.4 - - + -
367I THR* 4.2 7.9 - - - +
368I LEU* 1.3 85.6 - - - +
370I ASP* 1.3 63.1 + - - +
372I VAL* 3.5 13.5 - - + -
383I ILE* 5.5 1.8 - - + -
387I VAL* 3.7 26.0 - - + -
388I LEU 2.9 9.5 + - - +
389I GLN* 3.4 10.3 - - + +
390I VAL 2.8 26.3 + - - -
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Residues in contact with ASP 370 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298I VAL* 3.3 24.6 - - + +
344I ALA* 3.5 5.4 - - - +
345I THR* 2.8 30.5 + - - +
347I VAL* 3.6 21.3 - - + +
368I LEU* 4.3 0.4 - - + -
369I ILE* 1.3 75.3 - - - +
371I HIS* 1.3 103.3 + - - +
372I VAL 3.2 3.8 + - - -
390I VAL* 3.7 12.4 - - - +
392I ARG* 3.2 33.7 + - - -
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Residues in contact with HIS 371 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295I ASP* 5.6 0.2 + - - -
343I GLY 4.4 6.1 - - - +
344I ALA* 4.1 2.9 - - - -
345I THR* 3.2 28.9 + - + +
370I ASP* 1.3 103.1 + - + +
372I VAL* 1.3 63.4 + - - +
373I THR* 4.0 6.7 - - - +
376I MET* 3.7 12.1 - - - +
390I VAL 3.4 4.5 + - - -
392I ARG* 3.5 39.4 + - - +
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Residues in contact with VAL 372 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344I ALA* 4.2 2.9 - - + -
369I ILE* 3.5 32.5 - - + +
370I ASP 3.8 3.8 - - - +
371I HIS* 1.3 80.5 - - - +
373I THR* 1.3 64.1 + - - +
376I MET* 3.7 15.3 - - - -
379I TYR* 4.2 13.0 - - + -
389I GLN* 3.9 33.0 - - + +
390I VAL 3.2 11.6 + - - +
391I VAL* 3.1 46.4 - - + +
392I ARG 4.7 1.6 + - - -
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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
------------------------------------------------------------
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