Contacts of the strand formed by residues 157 - 162 (chain B) in PDB entry 3T0E
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 GLU 157 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B ILE* 1.3 80.7 - - - +
158B VAL* 1.3 62.0 + - - +
159B ARG* 3.8 30.0 + - - +
203B GLN 3.3 4.7 - - - +
204B VAL* 3.5 2.4 - - - -
205B GLU* 3.1 51.6 + - + +
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Residues in contact with VAL 158 (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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146B CYS* 4.3 2.0 - - - -
148B VAL* 3.9 15.5 - - + -
156B ILE* 4.0 12.2 + - + -
157B GLU* 1.3 79.1 - - - +
159B ARG* 1.3 63.6 - - - +
160B TRP* 5.4 1.1 - - + +
171B VAL* 6.1 0.3 - - - +
186B THR* 5.5 3.1 - - + -
188B VAL* 3.7 44.0 - - + +
202B CYS* 4.0 23.8 - - - -
203B GLN 3.2 3.6 - - - +
204B VAL* 3.7 22.0 - - + -
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Residues in contact with ARG 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B GLU* 3.8 26.9 + - - +
158B VAL* 1.3 79.9 - - - +
160B TRP* 1.3 63.9 + - - +
161B PHE* 3.9 7.7 + - + -
166B GLU* 2.8 47.9 + - + +
168B LYS* 5.0 7.3 - - - +
202B CYS* 5.0 0.2 - - - -
203B GLN* 3.2 55.6 + - - +
205B GLU* 4.2 10.0 + - - +
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Residues in contact with TRP 160 (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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130B VAL* 3.9 19.5 - - + -
144B LEU* 3.2 42.8 - - + -
145B VAL 4.1 4.9 - - - -
146B CYS* 3.7 22.9 - - + +
158B VAL* 5.4 0.7 - - + -
159B ARG* 1.3 76.2 - - - +
161B PHE* 1.3 65.6 + - - +
166B GLU* 3.6 5.4 - - - +
167B GLU* 3.1 33.2 + - + +
171B VAL* 4.0 20.2 - - + +
188B VAL* 3.4 27.3 + - + +
190B LEU* 3.2 45.7 - - + +
200B TYR* 4.2 2.7 - - + -
201B THR 2.8 41.3 - - - -
202B CYS* 4.1 8.7 - - + -
215B VAL 5.7 0.2 - - - -
216B GLU 6.4 0.9 - - - -
217B TRP* 5.6 1.6 - - + -
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Residues in contact with PHE 161 (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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159B ARG* 4.0 13.9 - - - -
160B TRP* 1.3 75.2 - - - +
162B ARG* 1.3 59.7 + - - +
163B ASN 3.8 0.6 + - - -
164B GLY* 4.6 15.5 - - - +
165B GLN 3.0 22.9 - - - +
166B GLU* 3.4 37.0 - - + -
167B GLU* 4.9 1.1 - - - -
190B LEU* 5.9 0.4 - - - -
200B TYR* 3.3 7.6 - - - -
201B THR* 2.8 56.5 + - + +
203B GLN* 3.1 47.3 - - + -
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Residues in contact with ARG 162 (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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160B TRP 4.4 0.2 - - - -
161B PHE* 1.3 71.9 - - - +
163B ASN* 1.3 84.2 + - - +
164B GLY 3.5 0.4 - - - -
165B GLN* 3.0 28.0 + - + +
166B GLU 6.0 0.2 - - - -
167B GLU* 2.9 49.1 + - + +
190B LEU* 6.4 0.2 - - + -
192B THR* 4.0 11.5 - - - +
193B VAL* 5.0 6.1 + - - +
198B GLU* 4.1 12.7 + - - +
200B TYR* 3.4 43.6 + - + -
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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