Contacts of the strand formed by residues 139 - 143 (chain B) in PDB entry 2ZUQ
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 139 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137B ALA 3.4 13.0 + - - -
138B PRO* 1.3 72.0 - - - +
140B VAL* 1.3 65.1 + - - +
141B SER* 4.0 5.4 + - - -
160B PHE 3.7 1.7 - - - +
161B LEU 4.4 0.2 - - - -
162B ASN* 3.0 42.0 + - - +
163B ASN* 4.7 5.9 - - - +
230B ILE* 6.0 0.2 - - - -
143C THR* 6.1 3.6 - - + +
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Residues in contact with VAL 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B PRO 3.8 3.8 + - - -
139B THR* 1.3 79.8 - - - +
141B SER* 1.3 71.5 + - - +
159B CYS* 3.7 6.1 - - + -
160B PHE 3.1 14.8 - - - +
161B LEU* 3.6 21.7 - - + +
219B CYS* 3.5 32.5 - - - +
221B ALA 5.5 0.9 - - - +
230B ILE* 3.8 36.0 - - + +
232B LYS* 3.6 30.9 - - + +
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Residues in contact with SER 141 (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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139B THR 4.0 4.4 + - - -
140B VAL* 1.3 83.5 - - - +
142B ILE* 1.3 59.8 + - - +
143B PHE* 3.1 27.4 - - - -
159B CYS* 3.3 16.3 - - - -
160B PHE* 3.3 14.2 + - - +
162B ASN* 5.7 1.2 - - - -
232B LYS* 3.8 15.9 - - - +
143C THR* 3.5 23.7 + - - +
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Residues in contact with ILE 142 (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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141B SER* 1.3 69.4 - - - +
143B PHE* 1.3 75.5 + - - +
144B PRO* 4.1 5.5 - - - +
157B VAL* 3.9 7.6 - - + -
158B VAL 3.6 7.4 - - - +
159B CYS* 3.7 10.7 - - + +
173B TRP* 3.6 28.9 - - + -
217B TYR* 4.5 1.1 - - + -
218B THR* 4.1 21.1 - - - +
232B LYS* 3.5 38.2 + - + +
233B SER 3.7 23.8 - - - +
234B PHE* 3.8 30.5 - - + -
132C PRO* 4.9 0.7 - - - +
133C VAL* 4.3 9.6 + - + +
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Residues in contact with PHE 143 (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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141B SER* 3.1 42.0 - - - -
142B ILE* 1.3 76.7 - - - +
144B PRO* 1.3 69.0 - - + +
156B SER 4.3 0.3 - - - +
157B VAL* 3.4 6.8 - - - +
158B VAL* 2.7 48.4 + - + +
160B PHE* 3.6 22.2 - + - -
130C LEU* 3.5 46.1 - - + +
131C ALA 3.9 6.3 - - - +
132C PRO* 4.2 12.3 - - + -
143C THR* 3.1 37.0 - - - -
144C LEU* 3.7 4.0 - - - -
145C GLY* 3.6 8.1 - - - -
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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