Contacts of the strand formed by residues 250 - 256 (chain B) in PDB entry 2ZUC
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 ALA 250 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89B ILE* 4.1 12.6 - - + -
104B ILE* 3.7 20.4 - - + -
105B GLU 3.4 20.6 - - - +
106B THR* 3.8 13.2 - - + +
108B THR 4.3 1.1 - - - -
205B LYS 2.9 17.2 + - - +
206B LEU* 3.1 6.1 - - + +
207B ILE 2.7 32.2 + - - -
249B ILE* 1.3 71.8 - - - +
251B VAL* 1.3 54.6 + - - +
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Residues in contact with VAL 251 (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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104B ILE* 5.4 0.5 - - - +
108B THR 3.5 8.1 + - - +
109B MET* 3.4 16.7 - - + -
110B THR* 2.9 27.2 + - - -
207B ILE* 3.4 21.5 - - + +
209B VAL* 5.4 0.4 - - + -
240B LEU* 3.8 41.5 - - + +
243B LEU* 5.2 1.1 - - + -
244B ALA* 3.3 33.0 - - + +
249B ILE* 4.0 6.1 - - + +
250B ALA* 1.3 75.5 - - - +
252B ILE* 1.3 75.5 + - - +
253B ILE* 4.7 0.2 - - + -
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Residues in contact with ILE 252 (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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104B ILE* 4.3 13.9 - - + -
110B THR* 3.4 11.2 - - - +
112B PHE* 4.1 18.8 - - + -
124B CYS* 4.6 17.9 - - - -
127B LEU* 3.0 41.5 - - + -
206B LEU* 3.3 26.7 - - + -
207B ILE 2.9 9.4 + - - +
208B VAL* 3.4 8.0 - - + -
209B VAL* 2.7 32.6 + - - +
251B VAL* 1.3 80.1 - - - +
253B ILE* 1.3 71.1 + - - +
254B THR* 4.7 0.7 - - + -
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Residues in contact with ILE 253 (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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109B MET* 3.5 42.4 - - + -
110B THR 3.0 6.2 + - - +
111B GLU* 3.2 30.4 - - + -
112B PHE 3.1 20.1 + - - -
209B VAL* 3.2 17.0 - - + +
212B VAL* 3.3 23.8 - - + -
237B LEU* 3.7 11.9 - - + -
240B LEU* 4.1 12.1 - - + -
251B VAL* 4.7 2.0 - - + -
252B ILE* 1.3 80.5 - - - +
254B THR* 1.3 66.1 + - - +
255B ASN* 6.2 0.4 - - + -
281B PRO* 3.9 7.0 - - + -
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Residues in contact with THR 254 (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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112B PHE* 3.0 19.5 - - + +
120B LYS* 3.7 32.8 - - + +
124B CYS* 3.7 24.0 - - - -
209B VAL 3.3 2.6 + - - -
210B ASP* 2.3 30.7 + - - +
211B SER* 2.9 32.7 + - - -
212B VAL* 3.3 8.1 + - - +
252B ILE* 4.7 3.6 - - + -
253B ILE* 1.3 79.8 - - - +
255B ASN* 1.3 61.6 + - - +
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Residues in contact with ASN 255 (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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111B GLU* 3.4 28.1 + - + +
112B PHE 3.2 4.9 + - - -
113B PHE* 3.0 30.4 - - + +
114B GLY 3.1 5.0 + - - +
120B LYS* 4.0 4.5 - - - +
211B SER* 4.8 1.3 - - - +
212B VAL* 5.0 2.5 - - + -
213B THR* 2.8 42.3 + - + +
217B ARG* 3.2 13.8 + - - +
253B ILE* 6.2 0.4 - - + -
254B THR* 1.3 77.0 - - - +
256B GLN* 1.3 64.8 + - - +
257B VAL* 3.5 21.5 - - - +
260B ARG* 4.6 11.9 - - - +
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Residues in contact with GLN 256 (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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114B GLY 3.5 11.0 - - - +
116B PHE* 3.7 41.8 - - - +
120B LYS* 3.1 27.3 + - - +
150B GLU* 5.7 4.8 + - - +
211B SER* 5.0 13.6 + - - +
213B THR* 4.6 1.6 + - - -
217B ARG* 2.5 38.4 + - - +
255B ASN* 1.3 73.3 + - - +
257B VAL* 1.3 66.6 + - - +
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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