Contacts of the strand formed by residues 306 - 312 (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 PHE 306 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A LYS 3.8 3.0 + - - +
35A ASN* 3.0 49.6 + - + -
36A LEU* 2.8 31.1 + - - +
37A ILE* 3.7 22.0 - - + -
141A LYS* 4.0 9.4 - - - +
142A SER 3.0 15.3 - - - +
296A LEU* 3.6 31.0 - - + -
299A LEU* 3.8 39.3 - - + +
300A SER* 4.2 16.2 - - - -
302A ASN 5.9 0.2 - - - -
305A GLY* 1.3 75.2 - - - +
307A PHE* 1.3 56.3 + - - +
308A LEU* 3.9 15.7 - - + -
345A THR* 4.1 15.7 - - + -
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Residues in contact with PHE 307 (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* 3.2 29.2 - - + -
38A ILE* 3.9 19.3 - - + -
100A LEU* 4.5 11.2 - - + -
132A VAL* 3.6 24.5 - - + -
133A MET* 3.4 37.9 - - + -
136A ALA* 3.8 20.2 - - + -
141A LYS* 4.6 0.8 - - + +
142A SER 2.9 5.5 + - - +
143A VAL* 3.2 9.0 - - + +
144A GLY 3.0 23.9 + - - -
159A THR* 4.7 2.0 - - + -
299A LEU* 4.2 1.9 - - - +
306A PHE* 1.3 75.4 - - - +
308A LEU* 1.3 74.9 + - - +
309A PHE* 4.0 13.0 - - + -
462A MET* 3.5 21.3 - - + -
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Residues in contact with LEU 308 (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 2.7 10.8 + - - +
37A ILE* 3.2 17.7 - - + +
38A ILE* 2.9 26.9 + - - +
39A PHE* 5.7 0.7 - - + -
144A GLY 3.6 8.5 - - - +
146A VAL* 3.6 22.4 - - + -
292A THR* 4.6 7.6 - - - +
295A ALA* 4.0 3.1 - - + -
296A LEU* 3.5 33.4 - - + -
299A LEU* 3.9 15.9 - - + -
306A PHE* 3.9 14.6 - - + -
307A PHE* 1.3 79.3 - - - +
309A PHE* 1.3 75.1 + - - +
310A VAL* 3.5 21.1 - - + -
341A ALA* 5.7 0.4 - - + -
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Residues in contact with PHE 309 (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* 3.5 20.6 - - + -
40A LEU* 4.2 16.4 - - + -
99A TYR* 4.3 6.1 - + - -
100A LEU* 4.1 9.6 - - + -
144A GLY 2.9 13.7 + - - +
145A VAL* 4.0 14.4 - - + -
146A VAL* 2.8 41.3 + - - +
147A THR* 4.4 0.9 - - - -
155A SER* 3.7 16.4 - - - -
156A PRO* 3.6 36.3 - - + -
159A THR* 4.0 17.5 - - + -
307A PHE* 4.0 13.4 - - + -
308A LEU* 1.3 74.5 - - - +
310A VAL* 1.3 57.4 + - - +
311A GLU* 3.6 31.6 - - + -
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Residues in contact with VAL 310 (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* 4.5 1.3 - - + -
38A ILE 3.0 7.3 + - - -
39A PHE* 3.1 32.5 - - + -
40A LEU* 2.8 31.2 + - - +
146A VAL* 3.2 5.8 - - + -
288A LEU* 4.0 17.9 - - + -
292A THR* 3.5 35.2 - - + -
308A LEU* 3.5 35.9 - - + -
309A PHE* 1.3 74.0 - - - +
311A GLU* 1.3 56.9 + - - +
334A PHE* 3.9 3.6 - - + -
337A ALA* 4.6 3.8 - - + -
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Residues in contact with GLU 311 (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* 3.1 19.2 - - + +
42A ASP* 3.2 11.1 - - - +
146A VAL 2.8 8.3 + - - -
147A THR* 2.6 25.2 + - - +
148A THR 3.5 15.9 + - - -
149A THR* 3.5 2.6 + - - -
155A SER* 3.0 12.2 + - - -
156A PRO* 3.4 18.4 - - - +
288A LEU* 3.4 15.9 - - - +
309A PHE* 3.6 17.7 - - + -
310A VAL* 1.3 74.8 - - - +
312A GLY* 1.3 58.6 + - - +
313A GLY* 3.0 20.1 + - - +
903A MG 2.1 29.6 - - - -
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Residues in contact with GLY 312 (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 2.9 9.4 + - - -
42A ASP 3.0 20.4 + - - -
148A THR* 4.0 2.0 - - - -
288A LEU* 3.7 14.8 - - - -
311A GLU* 1.3 68.6 - - - +
313A GLY* 1.3 62.1 + - - -
314A ARG 3.3 3.8 + - - -
315A ILE* 3.4 18.3 + - - +
330A GLU* 5.2 3.8 - - - -
334A PHE* 3.4 23.4 - - - -
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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