Contacts of the strand formed by residues 142 - 150 (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 SER 142 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A LYS* 4.4 0.8 + - - +
141A LYS* 1.3 73.7 - - - +
143A VAL* 1.3 62.6 + - - +
197A ASP* 3.1 19.5 + - - -
298A LEU 5.3 1.1 + - - -
299A LEU* 3.6 27.9 + - - -
302A ASN* 2.8 33.6 + - - +
305A GLY 3.0 7.2 + - - -
306A PHE* 3.0 6.2 - - - +
307A PHE 2.9 23.4 + - - -
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Residues in contact with VAL 143 (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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133A MET* 3.5 40.6 - - + +
136A ALA* 4.2 1.6 - - + -
137A LYS* 3.9 15.9 - - + +
141A LYS 4.0 5.2 - - - +
142A SER* 1.3 81.9 - - - +
144A GLY* 1.3 58.3 + - - +
194A MET* 3.8 13.0 - - + -
195A ASP 3.6 24.2 - - - +
196A ILE* 3.7 10.9 - - + +
197A ASP* 2.7 38.8 + - - +
198A VAL 3.2 5.5 + - - -
299A LEU* 3.7 4.0 - - - -
307A PHE* 3.2 12.6 - - + +
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Residues in contact with GLY 144 (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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133A MET* 4.0 3.9 - - - +
143A VAL* 1.3 75.3 - - - +
145A VAL* 1.3 67.0 + - - +
198A VAL* 3.3 13.2 - - - -
299A LEU* 3.8 18.9 - - - +
307A PHE 3.0 9.1 + - - +
308A LEU* 3.6 7.0 - - - -
309A PHE* 2.9 26.3 + - - +
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Residues in contact with VAL 145 (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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133A MET* 3.7 18.6 - - + -
144A GLY* 1.3 75.6 - - - +
146A VAL* 1.3 66.6 + - - +
147A THR* 4.8 4.5 - - + -
151A VAL* 5.0 10.5 - - + +
156A PRO* 3.5 33.0 - - + +
159A THR* 3.4 25.8 - - + +
160A TYR* 4.7 8.1 - - + -
190A LEU* 6.0 0.4 - - + -
196A ILE* 4.3 9.4 - - + -
198A VAL 2.8 9.5 + - - +
199A ILE* 3.5 9.1 - - + -
200A LEU 2.9 26.0 + - - -
309A PHE* 3.7 8.1 - - + -
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Residues in contact with VAL 146 (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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145A VAL* 1.3 82.2 - - - +
147A THR* 1.3 66.3 + - - +
198A VAL* 4.8 0.7 - - + -
200A LEU* 3.3 13.2 - - + +
288A LEU* 3.8 16.2 - - + -
291A MET* 3.7 35.0 - - + +
292A THR* 4.1 7.4 - - + +
295A ALA* 3.7 20.2 - - + -
308A LEU* 3.6 22.9 - - + -
309A PHE* 2.8 14.9 + - - +
310A VAL* 3.2 7.7 - - + -
311A GLU 2.8 23.9 + - - -
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Residues in contact with THR 147 (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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145A VAL* 4.8 0.9 - - + -
146A VAL* 1.3 79.6 - - - +
148A THR* 1.3 63.1 + - - +
149A THR* 3.0 29.6 + - - +
150A ARG 3.9 6.7 - - - +
151A VAL* 4.2 8.1 - - + -
156A PRO* 4.0 16.4 - - + -
200A LEU 3.0 9.0 + - - +
201A GLY* 3.0 27.2 - - - -
288A LEU* 4.3 1.6 - - - -
291A MET* 3.6 8.5 - - - +
309A PHE* 4.4 2.7 - - - -
311A GLU* 2.6 39.6 + - - +
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Residues in contact with THR 148 (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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147A THR* 1.3 72.7 + - - +
149A THR* 1.3 60.2 + - - +
274A MET* 2.8 42.9 + - + +
275A LYS 5.6 2.5 - - - +
288A LEU* 3.9 36.6 - - + +
291A MET* 4.4 5.4 - - + -
311A GLU 3.5 1.8 + - - -
312A GLY* 4.0 0.6 - - - -
313A GLY 3.0 24.1 + - - -
314A ARG* 3.5 24.1 + - - +
330A GLU* 4.5 11.1 + - - +
333A MET* 6.1 0.7 - - + -
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Residues in contact with THR 149 (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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147A THR* 3.0 18.9 + - - +
148A THR* 1.3 79.7 - - - +
150A ARG* 1.3 78.4 + - - +
151A VAL 3.3 0.5 + - - -
153A HIS* 3.3 21.7 - - + +
156A PRO* 4.3 0.2 - - - +
202A GLY 2.9 19.4 + - - -
273A ASP* 3.3 13.5 - - - -
311A GLU* 3.5 6.9 + - - +
313A GLY* 3.6 35.0 - - - +
314A ARG* 4.2 1.6 - - + -
317A HIS* 3.9 20.4 - - + +
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Residues in contact with ARG 150 (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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149A THR* 1.3 84.8 + - - +
151A VAL* 1.3 59.0 + - - +
152A GLN* 3.0 16.6 - - - +
153A HIS* 3.1 49.2 + - + +
156A PRO* 3.6 3.6 - - - +
169A TYR* 3.6 21.6 + - - -
202A GLY 3.5 9.0 - - - -
203A GLY* 3.8 7.6 - - - -
205A LYS* 5.2 1.2 - - - +
206A TYR* 3.1 34.9 + - + -
272A GLY* 3.4 29.2 - - - +
273A ASP* 2.8 42.7 + - - +
317A HIS* 4.8 1.2 - - - -
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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