Contacts of the strand formed by residues 180 - 189 (chain B) in PDB entry 1TW8
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 LEU 180 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B LYS* 3.1 4.4 - - - -
20B VAL* 2.8 54.1 + - + +
22B ARG* 4.2 6.1 - - + -
23B PRO* 6.2 1.6 - - + -
28B LEU* 3.7 23.6 - - + -
33B ALA 4.7 6.1 - - - +
34B GLY* 4.5 9.0 - - - -
36B PRO* 6.2 0.2 - - + -
37B PHE* 3.2 11.4 - - + -
173B TRP* 3.3 53.6 - - + -
174B GLU 3.8 4.9 - - - -
175B LEU* 3.9 8.7 - - + -
178B GLU 3.7 9.4 - - - +
179B ASP* 1.3 78.8 - - - +
181B VAL* 1.3 59.0 + - - +
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Residues in contact with VAL 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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17B GLY* 3.3 22.2 - - - +
18B GLN 3.1 17.0 - - - +
19B LYS* 4.7 4.9 - - + -
173B TRP* 4.0 3.6 - - - -
174B GLU* 3.2 35.5 + - + +
176B ASN* 4.3 20.6 - - + +
179B ASP 4.0 0.6 + - - -
180B LEU* 1.3 73.3 - - - +
182B CYS* 1.3 70.9 + - - +
183B VAL* 3.1 15.3 + - + +
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Residues in contact with CYS 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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15B LEU* 3.1 40.8 - - + +
16B ILE* 3.5 8.2 - - - +
17B GLY 2.9 26.2 + - - -
18B GLN 3.2 6.8 + - - +
37B PHE* 3.8 20.8 - - + -
171B VAL* 3.9 14.6 - - + -
172B ASP 3.2 11.0 - - - +
173B TRP* 4.0 3.6 - - - +
181B VAL* 1.3 72.9 - - - +
183B VAL* 1.3 57.9 + - - +
184B SER 3.1 27.1 - - - -
185B THR* 4.1 0.2 - - - -
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Residues in contact with VAL 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ILE* 3.9 19.2 - - - +
133B ILE* 3.7 30.7 - - + -
172B ASP 2.8 10.9 + - - +
174B GLU* 3.6 32.3 - - + +
181B VAL* 3.2 20.0 - - + +
182B CYS* 1.3 74.4 - - - +
184B SER* 1.3 71.7 + - - +
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Residues in contact with SER 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ILE* 4.2 9.6 - - - -
133B ILE* 4.7 0.2 - - - +
171B VAL* 4.0 0.2 - - - -
172B ASP* 2.5 44.4 + - - +
182B CYS* 3.1 15.3 - - - -
183B VAL* 1.3 86.3 - - - +
185B THR* 1.3 72.8 + - - +
213B ARG* 3.6 11.3 + - - -
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Residues in contact with THR 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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8B TYR* 3.0 36.4 + - + +
11B ILE* 6.3 0.2 - - + -
12B ASN* 3.9 25.5 + - + +
15B LEU* 3.9 21.0 - - + +
169B LEU* 3.6 17.3 - - + -
170B GLU 3.1 10.4 + - - +
171B VAL* 4.5 1.6 - - - -
172B ASP* 3.4 2.8 + - - -
182B CYS* 4.1 4.9 - - - -
184B SER* 1.3 86.1 + - - +
186B SER* 1.3 72.5 + - - +
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Residues in contact with SER 186 (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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8B TYR* 3.1 7.4 - - - -
168B TYR 3.9 0.2 - - - +
169B LEU* 3.3 5.5 - - - +
170B GLU* 2.6 47.0 + - - +
172B ASP* 4.7 1.0 + - - -
185B THR* 1.3 83.9 + - - +
187B PHE* 1.3 60.1 + - - +
212B VAL* 3.9 3.3 - - - +
213B ARG* 3.3 44.3 + - - +
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Residues in contact with PHE 187 (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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2B SER* 3.4 22.2 - - - -
4B ILE* 4.0 30.1 - - + -
5B LYS* 4.0 27.4 - - + -
8B TYR* 3.5 31.2 + + + -
124B GLU* 3.9 0.2 - - - -
126B LEU* 4.2 2.2 - - + -
167B ASN* 3.7 25.8 - - + -
168B TYR 3.3 15.9 - - - -
169B LEU* 4.5 12.6 - - + -
186B SER* 1.3 75.7 - - - +
188B ALA* 1.3 75.1 + - - +
189B GLU* 3.8 24.7 - - + -
212B VAL* 3.7 3.3 - - - +
217B GLN* 5.0 2.7 - - - +
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Residues in contact with ALA 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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167B ASN* 3.5 2.4 - - - +
168B TYR* 2.8 40.1 + - + +
187B PHE* 1.3 83.2 - - - +
189B GLU* 1.3 63.0 + - - +
190B LEU 3.9 0.3 + - - -
212B VAL* 3.4 24.2 - - + +
215B LEU* 3.8 24.7 - - + +
217B GLN* 3.8 15.5 - - + +
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Residues in contact with GLU 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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2B SER* 4.8 11.4 + - - -
5B LYS* 5.0 10.4 + - - +
165B ASP* 4.7 10.2 - - - +
167B ASN* 3.1 29.4 + - - +
187B PHE* 3.8 16.8 - - + -
188B ALA* 1.3 73.9 - - - +
190B LEU* 1.3 67.1 + - - +
191B PHE* 4.6 2.2 - - + +
192B LYS* 3.0 46.4 + - + +
193B SER* 3.6 1.2 + - - -
215B LEU* 4.5 1.7 - - - +
217B GLN* 2.9 32.9 + - - +
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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