Contacts of the strand formed by residues 328 - 331 (chain A) in PDB entry 4TZ3
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 HIS 328 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302A LEU* 3.3 44.0 - - + +
306A GLN* 3.2 25.7 + - + +
307A PHE* 3.2 26.7 - - + -
308A TYR* 2.7 24.8 + - - +
326A GLY 5.4 1.6 - - - -
327A LEU* 1.3 78.3 - - - +
329A LEU* 1.3 63.8 + - - +
346A ARG* 3.6 16.3 + - - -
348A ASN* 3.3 24.9 - - + -
349A THR* 3.7 5.1 - - - -
350A VAL* 3.0 23.3 + - + +
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Residues in contact with LEU 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A PHE* 3.3 13.2 - - - -
308A TYR* 3.6 22.0 - - + -
310A VAL* 4.5 2.9 - - + -
319A ILE* 3.8 42.4 - - + +
322A ALA* 4.7 1.6 - - + -
323A VAL* 3.9 20.9 - - + -
328A HIS* 1.3 82.9 - - - +
330A LEU* 1.3 58.9 + - - +
331A PHE* 3.7 28.9 - - + -
342A ILE* 4.4 8.5 - - + -
344A ILE* 4.7 6.1 - - + -
349A THR* 5.1 1.6 - - + -
350A VAL 3.0 12.3 + - - +
351A ALA* 4.3 11.7 - - + -
352A LEU* 3.0 24.1 + - - -
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Residues in contact with LEU 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A LEU* 3.5 31.9 - - + -
269A LEU* 4.6 9.9 - - + -
278A VAL* 4.8 8.3 - - + -
304A LEU* 4.0 16.8 - - + -
307A PHE* 4.0 11.9 - - + -
308A TYR 2.9 14.2 + - - +
309A VAL* 3.7 7.9 - - + +
310A VAL* 3.0 24.1 + - - +
329A LEU* 1.3 73.4 - - - +
331A PHE* 1.3 66.1 + - - +
332A THR* 3.5 2.9 + - + +
352A LEU* 3.3 38.8 - - + +
354A LEU* 3.9 26.9 - - + -
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Residues in contact with PHE 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A VAL* 3.9 12.8 - - + -
319A ILE* 3.9 26.2 - - + -
329A LEU* 3.7 38.8 - - + -
330A LEU* 1.3 76.0 - - - +
332A THR* 1.3 60.4 + - - +
336A TYR* 3.7 26.7 - + + -
342A ILE* 4.2 19.1 - - + -
351A ALA* 4.7 5.6 - - + -
352A LEU 2.8 19.0 + - - +
354A LEU* 2.9 32.6 + - - +
357A ALA* 3.7 17.7 - - + +
359A ILE* 4.6 10.3 - - + -
381A LEU* 3.9 28.7 - - + -
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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