Contacts of the strand formed by residues 187 - 200 (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 187 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184B THR* 3.8 20.6 - - - +
185B TYR 3.5 0.2 - - - -
186B LEU* 1.3 72.7 - - - +
188B LYS* 1.3 58.5 + - - -
189B GLN* 3.8 7.6 + - - -
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Residues in contact with LYS 188 (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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54B ALA* 5.6 6.4 - - - +
67B VAL* 5.2 2.9 - - - -
184B THR* 4.4 0.2 - - - -
185B TYR 3.0 20.5 + - - +
186B LEU* 2.8 49.8 + - - +
187B GLY* 1.3 72.0 - - - +
189B GLN* 1.3 59.2 + - - +
190B TYR* 3.0 50.1 - - + +
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Residues in contact with GLN 189 (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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182B SER* 3.6 19.4 + - - +
183B TYR 3.2 11.2 - - - +
184B THR* 3.1 35.4 + - - +
187B GLY 3.8 6.9 + - - +
188B LYS* 1.3 70.3 - - - +
190B TYR* 1.3 62.6 + - - +
191B PRO* 4.6 1.7 - - - +
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Residues in contact with TYR 190 (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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20B ASN 5.8 1.1 - - - -
21B GLU* 5.6 0.7 - - - -
22B ILE* 3.4 27.0 - - + +
67B VAL* 3.1 49.8 - - + +
68B PRO* 4.1 12.6 - - + -
182B SER* 3.2 6.1 - - - -
183B TYR* 2.7 37.5 + - - -
185B TYR* 3.6 23.7 + + + -
188B LYS* 3.0 57.6 - - + +
189B GLN* 1.3 73.5 - - - +
191B PRO* 1.3 70.4 - - + +
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Residues in contact with PRO 191 (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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20B ASN* 4.0 23.8 - - + +
21B GLU* 2.9 30.2 - - + +
22B ILE* 3.5 4.2 - - - +
181B ALA 3.5 7.6 - - - +
182B SER* 4.4 3.6 - - - +
189B GLN 4.6 1.8 - - - +
190B TYR* 1.3 93.2 - - + +
192B ILE* 1.3 66.3 + - - +
193B THR* 5.9 2.7 - - + -
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Residues in contact with ILE 192 (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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21B GLU* 3.9 6.5 + - - -
22B ILE* 3.5 22.9 - - + +
125B CYS* 6.2 0.2 - - - -
128B MET* 4.1 16.8 - - + -
131B PHE* 3.2 47.6 - - + -
179B CYS 3.6 0.2 - - - +
180B HIS* 3.3 2.4 - - - +
181B ALA* 2.9 40.3 + - + +
183B TYR* 3.8 9.2 - - + +
191B PRO* 1.3 86.5 - - - +
193B THR* 1.3 71.7 + - - +
194B ARG* 3.6 34.1 - - - +
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Residues in contact with THR 193 (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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18B SER* 3.9 8.7 + - - -
21B GLU* 3.1 27.6 + - - +
99B ASN* 5.7 0.3 + - - -
104B CYS 4.9 8.5 + - - +
105B TYR* 6.0 1.2 - - - +
178B THR* 5.1 4.5 - - - +
179B CYS 3.2 7.9 - - - -
180B HIS* 3.4 34.5 - - + +
191B PRO* 5.9 2.2 - - + -
192B ILE* 1.3 83.6 - - - +
194B ARG* 1.3 85.1 + - - +
195B VAL* 6.0 0.9 - - - +
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Residues in contact with ARG 194 (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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17B SER* 5.4 9.3 + - - +
18B SER 5.8 0.8 - - - +
21B GLU* 4.2 6.5 + - - -
22B ILE 5.4 3.8 + - - -
23B ASP* 4.5 11.3 + - - -
109B ALA 5.8 0.2 - - - -
111B PHE* 4.1 16.2 - - + -
125B CYS* 4.1 9.4 - - - -
126B PRO* 3.1 43.8 + - + +
127B TYR* 3.2 29.0 + - - +
128B MET* 3.7 7.8 - - - -
131B PHE* 3.2 21.6 - - - -
177B TYR 3.7 0.3 - - - +
178B THR* 3.1 24.9 - - - +
179B CYS* 3.1 23.5 + - - -
192B ILE* 3.6 16.0 - - - +
193B THR* 1.3 94.0 + - - +
195B VAL* 1.3 62.6 + - - +
196B ILE* 4.8 0.4 - - - +
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Residues in contact with VAL 195 (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* 3.5 41.3 - - + -
106B ASN 4.0 14.8 - - - +
109B ALA* 4.1 18.6 + - + +
110B ILE* 3.4 8.9 - - + -
111B PHE* 3.0 29.1 + - - -
176B ASN* 4.2 15.0 - - + +
177B TYR 3.0 15.7 - - - +
178B THR* 3.4 15.5 - - + -
193B THR* 6.0 0.7 - - - +
194B ARG* 1.3 75.3 - - - +
196B ILE* 1.3 61.4 + - - +
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Residues in contact with ILE 196 (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 PHE* 3.2 8.1 - - + +
113B GLN* 3.6 39.5 - - + +
123B LEU* 4.4 17.0 - - + -
124B VAL 3.5 27.8 - - - +
125B CYS* 4.2 4.9 - - - -
126B PRO* 4.3 7.6 - - + -
143B TRP* 3.6 31.9 - - + -
176B ASN* 3.4 1.9 - - - -
177B TYR* 2.8 44.4 + - + +
179B CYS* 4.5 3.6 - - - -
194B ARG 4.8 0.2 - - - +
195B VAL* 1.3 80.6 - - - +
197B GLU* 1.3 66.6 + - - +
198B PHE 3.3 2.3 + - - +
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Residues in contact with GLU 197 (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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110B ILE* 3.8 28.6 - - + +
111B PHE 3.0 8.6 + - - +
112B LYS* 3.7 31.1 - - + +
113B GLN 3.1 23.7 + - - +
175B GLY* 4.7 1.6 - - - +
176B ASN* 3.3 29.3 + - - +
195B VAL 4.2 0.8 - - - -
196B ILE* 1.3 71.7 - - - +
198B PHE* 1.3 60.6 + - - +
199B ILE* 3.6 17.1 + - + +
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Residues in contact with PHE 198 (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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113B GLN 3.3 11.2 - - - -
115B LEU* 3.4 44.4 - - + -
123B LEU* 3.8 19.3 - - + -
166B VAL* 4.6 8.3 - - + -
169B VAL* 3.6 25.8 - - + -
173B HIS* 2.9 47.6 - + + -
174B ARG* 3.4 25.2 + - - +
175B GLY 2.9 21.8 + - - +
177B TYR* 3.6 19.5 - + + -
196B ILE* 3.3 2.3 + - + +
197B GLU* 1.3 71.9 - - - +
199B ILE* 1.3 67.3 + - - +
200B THR* 4.0 5.2 - - + -
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Residues in contact with ILE 199 (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 LYS* 4.1 36.8 - - + -
113B GLN 2.9 7.5 + - - -
114B LYS* 2.9 59.2 - - + +
115B LEU 3.2 1.2 + - - -
174B ARG* 3.4 29.2 - - - +
197B GLU* 4.1 18.2 - - + +
198B PHE* 1.3 77.9 - - - +
200B THR* 1.3 64.7 + - - +
201B LEU* 5.4 1.1 - - + -
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Residues in contact with THR 200 (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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115B LEU 3.3 9.2 - - - -
117B VAL* 3.9 15.4 - - - +
169B VAL* 3.8 13.5 - - + -
170B ALA 3.0 27.6 - - - +
171B GLU* 2.8 25.5 + - - -
174B ARG* 3.1 34.5 + - + -
198B PHE* 4.0 11.0 - - + -
199B ILE* 1.3 78.7 - - - +
201B LEU* 1.3 63.6 + - - +
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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