Contacts of the strand formed by residues 331 - 335 (chain B) in PDB entry 1ZQ1
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 GLY 331 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306B LYS 3.8 4.8 + - - +
307B VAL* 3.1 23.4 - - - +
308B ALA 3.1 10.9 + - - -
329B TYR* 3.5 2.2 - - - -
330B LYS* 1.3 81.9 - - - +
332B ILE* 1.3 67.6 + - - +
358B VAL* 4.1 0.2 - - - -
359B ALA 3.2 10.1 - - - -
402B LEU* 3.7 5.4 - - - -
406B LEU* 3.4 15.9 - - - +
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Residues in contact with ILE 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B ALA* 3.4 9.9 - - + +
310B VAL* 4.2 18.4 - - + -
321B ILE* 4.6 20.6 - - + +
324B LEU* 3.8 35.4 - - + -
325B VAL* 4.8 6.3 - - + +
329B TYR* 4.7 5.8 - - + -
331B GLY* 1.3 79.3 - - - +
333B VAL* 1.3 62.8 + - - +
334B ILE* 3.8 21.7 + - + -
353B ALA* 5.0 2.5 - - + -
358B VAL* 4.1 17.9 - - + -
359B ALA 2.6 10.9 + - - +
360B VAL* 3.3 11.0 - - + +
361B CYS 2.9 24.9 + - - +
402B LEU* 3.7 1.2 - - - +
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Residues in contact with VAL 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B VAL* 4.6 2.2 - - + -
308B ALA 2.9 9.9 + - - +
309B LEU* 3.4 26.5 - - + +
310B VAL 2.9 24.6 + - - -
332B ILE* 1.3 71.3 - - - +
334B ILE* 1.3 61.9 + - - +
361B CYS* 3.7 12.6 - - + +
363B THR* 3.8 29.4 - - + +
395B PRO 4.1 1.6 - - - +
398B ALA* 3.5 33.4 - - + +
399B TYR* 3.5 11.4 - - - -
402B LEU* 3.6 20.4 - - + -
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Residues in contact with ILE 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B VAL* 3.4 15.7 - - + +
312B VAL* 3.8 20.4 - - + -
321B ILE* 4.8 8.7 - - + -
332B ILE* 4.1 15.7 - - + -
333B VAL* 1.3 75.1 - - - +
335B GLU* 1.3 61.8 + - - +
336B GLY* 2.8 13.2 + - - +
342B THR* 4.1 1.1 - - - +
350B ILE* 3.7 32.8 - - + -
360B VAL* 3.8 17.9 - - + -
361B CYS 2.8 11.5 + - - +
362B MSE 3.5 31.9 - - + +
363B THR* 2.8 28.1 + - - -
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Residues in contact with GLU 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A ARG* 5.1 1.4 + - - -
311A LYS* 2.6 48.3 + - - +
335A GLU* 5.2 1.0 - - - +
255B ARG* 4.8 0.3 + - - -
309B LEU* 4.0 10.8 - - + +
310B VAL 2.7 10.3 + - - +
311B LYS* 3.7 27.8 + - + +
312B VAL* 3.2 21.0 + - - +
333B VAL 3.8 1.6 + - - -
334B ILE* 1.3 70.1 - - - +
336B GLY* 1.3 65.4 + - - +
363B THR* 3.3 5.4 - - - +
364B SER 4.5 0.2 - - - +
365B GLN* 3.7 26.4 - - - +
367B ILE* 4.7 5.2 - - - +
395B PRO* 3.7 30.1 - - + +
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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
------------------------------------------------------------
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