Contacts of the strand formed by residues 155 - 160 (chain 2) in PDB entry 1ZBE
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 THR 155 (chain 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262 THR* 3.2 38.1 + - - +
282 SER 4.1 5.5 + - - +
292 SER* 4.8 4.1 - - - -
302 VAL* 4.3 8.8 + - - +
1082 GLU* 3.6 23.1 - - + +
1092 VAL 3.3 11.7 - - - +
1102 SER* 4.9 6.3 - - - -
1462 GLN* 4.3 1.4 - - - +
1482 ILE* 4.3 0.9 - - - -
1532 ASN* 3.0 20.7 - - - +
1542 MET* 1.3 86.5 + - - +
1562 ALA* 1.3 73.3 + - - +
1572 HIS* 5.2 2.7 - - + -
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Residues in contact with ALA 156 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1082 GLU* 3.3 2.9 - - - -
1092 VAL* 2.7 34.2 + - + +
1232 VAL* 3.6 39.7 - - + -
1462 GLN* 3.2 17.7 - - + +
1472 PHE 4.7 1.1 - - - +
1482 ILE* 3.7 13.0 - - + +
1532 ASN* 4.9 0.4 - - - -
1552 THR* 1.3 77.3 - - - +
1572 HIS* 1.3 61.5 + - - +
1582 ILE* 5.2 0.7 - - - -
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Residues in contact with HIS 157 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152 LEU* 4.2 8.7 - - + -
172 THR* 3.3 27.6 + - - +
292 SER* 6.4 1.1 - - - -
312 GLY 3.9 14.1 - - - +
322 VAL* 3.4 21.6 - - + +
332 THR 3.0 22.5 + - - -
612 PHE* 5.5 0.6 - - - -
1062 ASP* 2.7 39.0 + - - -
1072 VAL 3.1 14.1 + - - -
1082 GLU* 4.2 20.8 - - + +
1462 GLN* 2.8 17.0 + - - -
1552 THR* 5.2 3.4 - - + -
1562 ALA* 1.3 76.1 - - - +
1582 ILE* 1.3 63.7 + - - +
1592 THR* 3.6 7.4 + - - -
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Residues in contact with ILE 158 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332 THR* 3.3 15.0 - - + +
1052 TRP 4.0 0.9 - - - +
1072 VAL* 2.8 44.8 + - + +
1232 VAL* 3.5 43.1 - - + +
1242 ALA* 4.0 5.2 - - - -
1252 MET* 4.0 25.4 - - + +
1442 PRO* 3.9 17.9 - - + +
1452 HIS* 3.8 20.4 - - - -
1462 GLN* 4.6 3.4 - - + -
1562 ALA 5.2 0.2 - - - -
1572 HIS* 1.3 81.1 - - - +
1592 THR* 1.3 67.4 + - - +
1602 VAL* 4.0 11.7 - - + -
1792 LEU* 5.6 0.2 - - + -
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Residues in contact with THR 159 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322 VAL* 3.5 14.8 - - - +
332 THR 2.8 9.2 + - - -
342 TYR* 3.4 32.5 + - + -
352 GLY 3.0 23.0 + - - -
372 SER 4.9 0.7 - - - +
1052 TRP 3.4 10.5 - - - +
1062 ASP* 2.7 27.8 + - + +
1572 HIS* 3.6 0.5 - - - -
1582 ILE* 1.3 73.0 - - - +
1602 VAL* 1.3 67.3 + - - +
1612 PRO* 4.5 0.7 - - - +
2062 THR* 5.5 4.9 - - + +
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Residues in contact with VAL 160 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352 GLY* 4.3 11.2 - - - -
402 GLU* 4.3 0.9 - - - +
1042 GLY* 3.5 2.1 - - - -
1052 TRP* 2.9 44.5 + - + +
1072 VAL* 5.8 0.2 - - + -
1252 MET* 3.7 37.9 - - + -
1442 PRO* 4.5 2.2 - - + -
1582 ILE* 4.0 11.6 - - + -
1592 THR* 1.3 85.0 - - - +
1612 PRO* 1.3 65.7 - - + +
1772 TRP* 3.6 41.7 - - + +
2062 THR* 4.4 2.1 + - - -
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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