Contacts of the strand formed by residues 175 - 185 (chain B) in PDB entry 1ITB
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 GLY 175 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145B LYS* 4.4 1.8 - - - -
146B ASP* 3.9 10.8 - - - -
173B HIS 3.6 0.8 + - - -
174B ARG* 1.3 77.1 - - - +
176B ASN* 1.3 67.7 + - - -
177B TYR* 3.2 14.1 - - - -
197B GLU* 5.1 1.7 - - - +
198B PHE 2.9 28.8 + - - -
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Residues in contact with ASN 176 (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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105B TYR* 3.6 41.6 - - + +
107B ALA* 5.4 2.8 - - - +
110B ILE* 3.4 29.3 - - - +
144B TYR 4.1 0.2 - - - +
146B ASP* 2.8 39.6 + - - +
147B CYS 4.6 0.9 + - - -
175B GLY* 1.3 71.6 - - - -
177B TYR* 1.3 60.8 + - - +
178B THR* 5.3 1.0 + - - +
195B VAL* 4.2 4.9 - - + +
196B ILE 3.4 2.5 - - - -
197B GLU* 3.3 34.1 + - - +
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Residues in contact with TYR 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B LEU* 4.1 7.9 - - + -
143B TRP* 4.7 9.2 - + + -
144B TYR 3.1 5.6 - - - -
145B LYS* 3.4 34.8 - - + +
150B LEU* 3.8 13.2 - - + -
157B PHE* 4.2 8.2 - + - -
164B LEU* 3.7 31.0 - - + -
166B VAL* 5.1 0.6 - - + +
173B HIS* 2.5 48.7 + - - +
175B GLY 3.2 17.7 - - - -
176B ASN* 1.3 75.5 - - - +
178B THR* 1.3 61.7 + - - +
194B ARG 3.7 0.2 - - - +
195B VAL* 3.0 7.4 - - - +
196B ILE* 2.8 43.5 + - + +
198B PHE* 3.6 20.5 - + + -
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Residues in contact with THR 178 (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 CYS* 4.3 13.4 - - - +
105B TYR* 4.2 19.5 - - + -
142B GLN 3.7 0.9 - - - +
143B TRP* 3.4 9.3 - - - -
144B TYR* 2.8 52.4 + - - +
147B CYS 5.1 1.0 + - - -
176B ASN 5.3 0.6 + - - +
177B TYR* 1.3 79.6 - - - +
179B CYS* 1.3 61.5 + - - +
180B HIS* 3.4 20.7 + - - +
193B THR* 5.1 3.6 - - - +
194B ARG 3.1 12.1 - - - +
195B VAL* 3.4 21.8 - - + -
196B ILE* 5.8 0.2 - - - -
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Residues in contact with CYS 179 (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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125B CYS* 2.0 54.0 - - - -
141B LEU* 3.5 14.8 - - + -
142B GLN 3.3 4.9 - - - -
143B TRP* 3.6 19.5 - - + -
178B THR* 1.3 72.5 - - - +
180B HIS* 1.3 69.5 + - - +
192B ILE 3.6 0.5 - - - +
193B THR* 3.2 19.6 - - - -
194B ARG* 3.1 23.2 + - - -
196B ILE* 4.5 2.5 - - - -
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Residues in contact with HIS 180 (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 CYS* 5.2 11.7 + - + -
140B LYS 3.5 2.4 - - - +
141B LEU* 3.3 8.7 - - - +
142B GLN* 2.8 57.0 + - - +
144B TYR* 3.1 33.1 + + + -
178B THR* 3.4 26.6 + - - +
179B CYS* 1.3 99.8 - - - +
181B ALA* 1.3 61.7 + - - +
192B ILE 3.3 3.4 - - - +
193B THR* 3.4 27.1 - - + +
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Residues in contact with ALA 181 (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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128B MET* 3.8 20.2 - - + -
139B PRO* 3.6 31.2 - - + -
140B LYS 4.2 7.4 - - - +
141B LEU* 4.7 3.6 - - + -
179B CYS 4.3 0.2 + - - -
180B HIS* 1.3 75.9 - - - +
182B SER* 1.3 61.6 + - - +
183B TYR 4.1 0.7 - - - -
191B PRO* 3.5 4.0 - - - +
192B ILE* 2.9 39.3 + - + +
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Residues in contact with SER 182 (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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134B GLU* 4.0 8.3 - - - +
139B PRO* 4.5 10.8 - - - +
140B LYS 5.1 0.8 + - - -
181B ALA* 1.3 76.9 - - - +
183B TYR* 1.3 59.6 + - - +
184B THR* 3.9 4.3 + - - -
189B GLN* 3.6 23.2 + - - +
190B TYR 3.2 12.9 + - - -
191B PRO* 4.9 1.7 - - - +
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Residues in contact with TYR 183 (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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22B ILE* 3.1 30.7 - - + +
65B TRP* 3.5 40.1 - + - -
130B PHE 3.8 8.5 + - - -
131B PHE* 3.4 31.9 - + + -
133B ASN* 3.0 33.5 + - - +
134B GLU* 3.5 15.0 - - - -
139B PRO* 5.8 2.5 - - + -
181B ALA 4.1 1.2 - - - -
182B SER* 1.3 71.0 - - - +
184B THR* 1.3 70.3 + - - +
185B TYR* 3.4 22.1 + + + -
189B GLN* 3.2 1.2 - - - -
190B TYR* 2.7 40.3 + - - +
192B ILE* 3.8 10.7 - - + +
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Residues in contact with THR 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B GLU* 3.3 33.1 + - - +
182B SER 4.5 2.3 + - - -
183B TYR* 1.3 79.3 - - - +
185B TYR* 1.3 60.2 + - - +
186B LEU 4.1 0.9 + - - -
187B GLY* 3.8 28.3 - - - +
189B GLN* 3.1 35.8 + - - +
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Residues in contact with TYR 185 (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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22B ILE* 5.1 5.8 - - + -
53B GLN* 4.1 7.3 + - - +
58B HIS* 3.0 38.2 - + - -
60B HIS* 3.9 22.0 - + - +
65B TRP* 4.0 40.1 - + + -
67B VAL* 4.5 13.0 - - + -
183B TYR* 3.4 20.1 + + + -
184B THR* 1.3 74.5 - - - +
186B LEU* 1.3 98.4 + - + +
188B LYS* 3.0 26.4 + - - +
190B TYR* 3.6 22.5 - + + -
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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