Contacts of the strand formed by residues 35 - 41 (chain A) in PDB entry 1ZEB
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 ASN 35 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A ALA* 3.5 8.8 - - - +
34A LYS* 1.3 89.9 - - - +
36A LEU* 1.3 63.0 + - - +
305A GLY* 3.1 12.6 - - - -
306A PHE* 3.0 58.2 + - + +
345A THR* 5.5 1.4 - - - -
349A ASP* 3.0 14.3 + - - -
350A THR* 3.1 28.6 + - + +
351A LEU 3.0 23.2 + - - -
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Residues in contact with LEU 36 (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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33A ALA* 4.1 3.8 - - + -
34A LYS 5.6 0.4 - - - +
35A ASN* 1.3 82.5 - - - +
37A ILE* 1.3 60.3 + - - +
38A ILE 4.3 0.2 - - - -
132A VAL* 4.0 6.3 - - + -
136A ALA* 5.3 0.9 - - + -
141A LYS* 5.6 2.5 - - + -
306A PHE 2.8 9.4 + - - +
307A PHE* 3.2 24.1 - - + -
308A LEU 2.7 32.2 + - - -
351A LEU* 3.5 28.7 - - + -
462A MET* 3.5 44.2 - - + +
465A ALA* 4.5 0.2 - - + -
466A ALA* 3.7 22.2 - - + -
468A LEU* 4.0 14.6 - - + -
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Residues in contact with ILE 37 (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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36A LEU* 1.3 79.7 - - - +
38A ILE* 1.3 66.4 + - - +
39A PHE* 3.4 41.7 - - + -
296A LEU* 4.4 7.9 - - + -
306A PHE* 3.7 26.2 - - + -
308A LEU* 3.2 22.7 - - + +
310A VAL* 4.5 0.4 - - + -
341A ALA* 4.5 4.0 - - + -
345A THR* 4.3 13.7 - - + +
350A THR* 3.8 22.2 - - + -
351A LEU 2.9 8.4 + - - +
352A SER* 3.3 10.5 - - - +
353A LEU* 2.9 25.9 + - - -
462A MET* 3.9 5.8 - - - +
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Residues in contact with ILE 38 (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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37A ILE* 1.3 74.5 - - - +
39A PHE* 1.3 71.3 + - - +
40A LEU* 4.0 3.3 + - + +
99A TYR* 3.5 36.6 - - + +
100A LEU* 4.2 2.5 - - + -
307A PHE* 3.9 23.3 - - + -
308A LEU 2.9 9.7 + - - +
309A PHE* 3.5 22.7 - - + -
310A VAL 3.0 25.8 + - - +
353A LEU* 3.4 9.2 - - + +
355A THR* 4.4 10.1 - - + -
458A ILE* 3.8 24.0 - - + -
462A MET* 3.9 14.2 - - + +
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Residues in contact with PHE 39 (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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37A ILE* 3.4 28.7 - - + -
38A ILE* 1.3 74.6 - - - +
40A LEU* 1.3 60.4 + - - +
74A PHE* 4.8 1.1 - + - -
292A THR* 5.1 0.7 - - - -
310A VAL* 3.1 34.5 - - + -
334A PHE* 3.5 18.5 - + + -
337A ALA 4.2 2.7 - - - -
338A ILE* 3.6 35.7 - - + -
341A ALA* 3.4 32.5 - - + -
342A GLY 5.4 0.2 - - - -
352A SER* 4.0 20.6 - - - -
353A LEU 2.7 20.3 + - - +
354A VAL* 3.3 15.1 - - + -
355A THR 2.9 27.5 + - - +
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Residues in contact with LEU 40 (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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38A ILE* 3.9 4.5 - - + -
39A PHE* 1.3 71.1 - - - +
41A GLY* 1.3 60.6 + - - +
42A ASP* 3.7 27.4 - - + +
99A TYR* 3.4 44.0 - - + +
309A PHE* 4.2 16.6 - - + -
310A VAL 2.8 11.5 + - - +
311A GLU* 3.1 17.7 - - + +
312A GLY 2.9 24.4 + - - -
334A PHE* 3.4 2.9 - - - -
355A THR* 3.4 27.4 - - + -
356A ALA 3.7 1.8 - - - -
357A ASP* 3.6 22.9 - - + +
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Residues in contact with GLY 41 (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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40A LEU* 1.3 70.7 - - - +
42A ASP* 1.3 66.3 + - - -
43A GLY 3.1 3.8 + - - -
44A MET* 3.2 12.4 + - - -
312A GLY 4.0 0.2 - - - -
315A ILE* 3.8 14.8 - - - -
334A PHE* 3.2 22.2 - - - -
355A THR 2.8 13.8 + - - -
356A ALA* 3.1 21.3 - - - +
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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