Contacts of the strand formed by residues 260 - 269 (chain B) in PDB entry 1ZHH
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 VAL 260 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A GLN* 3.3 37.0 - - + +
24A VAL 4.1 5.4 - - - +
25A LEU* 3.9 11.2 - - + -
26A ASN 3.3 36.1 - - - +
165A ARG* 3.5 24.7 - - - +
256B VAL* 3.4 5.4 - - - -
257B VAL 2.9 35.1 + - - +
258B ASN 3.7 0.7 - - - +
259B ALA* 1.3 76.5 - - - +
261B THR* 1.3 64.1 + - - +
262B THR* 3.5 3.8 + - - +
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Residues in contact with THR 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A GLN* 3.0 20.3 + - - -
254B PRO* 5.5 7.2 - - + -
255B ILE 4.4 2.9 - - - +
256B VAL* 4.4 17.3 - - + +
259B ALA 3.8 4.4 + - - -
260B VAL* 1.3 71.4 - - - +
262B THR* 1.3 71.1 + - - +
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Residues in contact with THR 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A GLN* 4.0 19.1 - - - +
25A LEU* 4.0 18.8 - - + -
155B TYR* 4.9 7.2 - - + -
254B PRO* 5.5 2.1 - - - +
255B ILE* 2.7 32.4 + - + +
257B VAL* 4.6 9.2 - - + -
260B VAL 3.9 8.5 - - - +
261B THR* 1.3 87.3 - - - +
263B GLU* 1.3 61.2 + - - +
264B LEU* 3.1 34.6 + - + +
265B CYS* 5.8 0.5 - - - -
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Residues in contact with GLU 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A GLN* 5.0 0.4 + - - -
155B TYR* 2.5 42.6 + - + +
157B ASN* 3.3 22.3 + - - +
214B VAL 3.8 0.3 - - - +
215B ALA* 3.5 15.2 - - + +
216B ASN* 3.2 40.6 + - + +
262B THR* 1.3 73.1 - - - +
264B LEU* 1.3 63.4 + - - +
265B CYS* 3.9 5.8 + - - -
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Residues in contact with LEU 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B PHE* 5.0 4.0 - - + -
155B TYR* 3.8 38.8 - - + +
168B LEU* 4.6 6.5 - - + -
192B LEU* 3.7 25.1 - - + -
213B LEU* 4.4 7.9 - - + -
214B VAL 3.3 5.6 - - - +
215B ALA* 4.0 2.5 - - + -
220B LEU* 3.7 29.4 - - + -
254B PRO* 3.7 1.0 - - - +
255B ILE* 3.0 43.9 + - + +
262B THR* 3.1 21.1 + - + +
263B GLU* 1.3 80.7 - - - +
265B CYS* 1.3 65.8 - - - +
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Residues in contact with CYS 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212B VAL 3.8 0.7 - - - +
213B LEU* 3.6 5.7 - - - +
214B VAL* 2.8 46.5 + - + +
252B GLU* 5.6 8.1 - - + +
253B THR 3.6 7.9 - - - +
254B PRO* 3.9 22.4 - - - -
255B ILE* 4.4 1.1 - - - +
262B THR 5.8 0.4 - - - -
263B GLU 4.6 5.4 - - - -
264B LEU* 1.3 83.6 - - - +
266B LEU* 1.3 66.2 + - - +
267B LEU* 4.0 8.7 - - + -
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Residues in contact with LEU 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B ILE* 3.9 40.5 - - + +
61B HIS* 5.2 0.9 - - - +
64B PHE* 4.2 15.0 - - + -
199B MET* 5.0 0.2 - - + -
202B LEU* 4.2 21.8 - - + -
211B VAL* 4.1 16.2 - - + -
212B VAL 3.7 1.3 - - - +
213B LEU* 3.4 39.3 - - + -
251B ILE 3.6 2.8 - - - +
252B GLU* 3.7 0.7 - - - -
253B THR* 2.9 41.4 + - + +
255B ILE* 3.8 21.7 - - + +
265B CYS* 1.3 71.7 - - - +
267B LEU* 1.3 60.9 + - - +
268B THR 4.0 0.4 + - - -
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Residues in contact with LEU 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B VAL* 3.2 5.3 - - - +
212B VAL* 2.8 44.9 + - + +
214B VAL* 3.8 17.0 - - + -
235B VAL* 4.1 25.1 - - + +
236B LEU* 3.2 36.6 - - + -
250B VAL 5.4 3.4 - - - +
251B ILE 3.4 4.3 - - - +
252B GLU* 3.6 44.2 - - + +
265B CYS* 5.0 7.0 - - + +
266B LEU* 1.3 73.6 - - - +
268B THR* 1.3 63.4 + - - +
269B VAL* 4.3 1.4 + - - +
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Residues in contact with THR 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B THR* 3.9 10.5 - - + +
60B ILE* 3.5 43.7 - - + +
208B VAL* 4.3 23.3 - - + -
210B ASN 3.6 5.2 - - - -
211B VAL* 4.4 9.9 - - + -
250B VAL* 2.9 28.6 + - - +
251B ILE* 3.2 27.2 + - - +
266B LEU 4.0 0.2 - - - -
267B LEU* 1.3 76.2 - - - +
269B VAL* 1.3 63.5 + - - +
270B GLN* 5.0 0.8 + - - -
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Residues in contact with VAL 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B VAL* 3.8 3.0 - - - +
209B ASP* 3.1 29.5 + - + +
210B ASN* 3.0 20.8 + - + +
211B VAL* 5.0 0.7 - - - +
212B VAL* 5.6 1.8 - - + -
230B TYR* 3.7 35.4 - - + +
235B VAL* 3.7 35.2 - - + -
250B VAL* 3.9 8.3 - - + +
267B LEU 5.0 1.3 - - - +
268B THR* 1.3 76.5 - - - +
270B GLN* 1.3 62.3 + - - +
271B ASP* 4.1 20.6 - - - +
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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