Contacts of the strand formed by residues 235 - 245 (chain B) in PDB entry 1TKW
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 235 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25B HIS* 5.8 0.9 - - - -
27B ALA* 3.0 20.2 - - - -
29B LYS* 4.1 10.8 - - - -
153B ASN* 3.1 16.2 + - - +
154B ARG* 3.0 33.8 + - - +
232B ASN* 4.7 0.7 - - - -
234B GLY* 1.3 75.2 - - - -
236B PHE* 1.3 60.1 + - - -
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Residues in contact with PHE 236 (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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19B ILE* 3.7 22.4 - - + -
21B CYS* 3.6 28.7 - - + -
22B ALA* 4.1 22.9 - - + -
25B HIS* 3.7 18.8 - - + +
27B ALA 2.6 10.1 + - - +
28B SER* 3.3 11.6 + - - -
29B LYS 3.1 17.1 + - - -
151B GLY* 3.4 23.8 - - - -
152B GLY 3.1 36.8 - - - -
153B ASN* 3.5 17.2 - - + +
235B GLY* 1.3 74.3 - - - -
237B GLY* 1.3 67.7 + - - +
238B GLN* 4.1 17.7 - - + -
253B HEC 4.6 0.7 - - + -
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Residues in contact with GLY 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B SER* 5.1 2.5 - - - -
29B LYS 3.0 19.1 + - - -
30B PRO* 5.1 0.4 - - - -
31B VAL* 3.1 12.0 - - - +
152B GLY 3.0 33.0 + - - -
236B PHE* 1.3 85.7 - - - +
238B GLN* 1.3 60.5 + - - -
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Residues in contact with GLN 238 (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 2.8 27.7 + - - -
18B ARG* 3.7 27.8 + - - +
19B ILE* 3.5 23.0 + - + +
22B ALA* 5.5 1.7 - - - +
31B VAL* 4.1 10.3 + - - +
149B TYR* 6.3 0.8 - - - -
150B VAL 3.2 13.7 - - - +
236B PHE* 4.1 9.5 - - + -
237B GLY* 1.3 75.7 - - - -
239B GLY* 1.3 60.3 + - - +
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Residues in contact with GLY 239 (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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31B VAL* 4.8 8.9 - - - +
32B ASP* 6.2 0.2 - - - -
33B ILE* 4.6 4.7 - - - -
149B TYR* 3.7 3.8 - - - +
150B VAL* 3.0 41.8 + - - +
238B GLN* 1.3 75.8 - - - +
240B ASP* 1.3 65.7 + - - +
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Residues in contact with ASP 240 (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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33B ILE* 4.3 10.1 - - - +
147B PRO* 6.3 0.2 - - + -
148B ILE 3.0 11.9 - - - +
149B TYR* 3.6 25.0 - - + -
239B GLY* 1.3 78.7 - - - +
241B ALA* 1.3 65.0 + - - +
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Residues in contact with ALA 241 (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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33B ILE* 4.3 16.2 - - + +
35B VAL* 4.2 26.2 - - + +
147B PRO* 3.5 4.2 - - - +
148B ILE* 2.8 44.8 + - + -
240B ASP* 1.3 77.7 - - - +
242B GLU* 1.3 61.1 + - - +
243B ILE 4.2 0.2 - - - -
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Residues in contact with GLU 242 (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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35B VAL* 5.3 2.1 - - - +
36B PRO 4.8 3.1 - - - +
37B GLN* 4.2 12.5 + - - +
145B LYS* 3.2 51.4 + - + +
146B TYR 3.3 13.2 - - - +
147B PRO* 4.8 2.5 - - + -
148B ILE* 4.6 1.1 - - - -
241B ALA* 1.3 77.4 - - - +
243B ILE* 1.3 61.8 + - - +
244B VAL* 5.2 2.9 - - - +
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Residues in contact with ILE 243 (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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35B VAL* 3.6 22.9 - - + -
36B PRO 3.8 9.9 - - - +
37B GLN 4.0 2.5 - - - +
39B VAL* 3.6 41.3 - - + +
45B PHE* 3.9 19.7 - - + -
78B PRO* 5.2 1.3 - - + -
81B PHE* 4.6 14.8 - - + -
144B LEU 3.6 1.6 - - - +
145B LYS* 3.3 2.0 - - - -
146B TYR* 2.7 58.3 + - + +
148B ILE* 3.6 18.3 - - + +
242B GLU* 1.3 75.5 - - - +
244B VAL* 1.3 66.0 + - - +
245B LEU 3.8 1.1 + - - +
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Residues in contact with VAL 244 (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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37B GLN* 3.1 24.8 + - + +
38B ALA* 3.3 11.1 - - + +
39B VAL 3.1 19.2 + - - -
144B LEU* 3.6 7.9 - - - +
145B LYS* 3.6 37.9 - - + +
242B GLU* 5.2 2.7 - - - +
243B ILE* 1.3 75.9 - - - +
245B LEU* 1.3 68.2 + - - +
246B GLN* 2.9 19.3 + - + +
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Residues in contact with LEU 245 (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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39B VAL* 3.8 10.3 - - + +
40B LEU 4.9 1.8 - - - +
41B PRO* 5.0 2.2 - - + -
81B PHE* 3.5 28.0 - - + -
132B ALA* 4.0 13.2 - - + -
133B PRO* 4.0 15.9 - - + +
135B PRO* 4.2 10.3 - - + -
141B VAL* 3.9 20.9 - - + -
142B HIS 3.3 27.6 - - - +
143B PHE* 3.3 41.2 - - + +
144B LEU 3.0 14.8 + - - +
146B TYR* 4.1 9.3 - - + -
243B ILE* 3.8 3.0 + - - +
244B VAL* 1.3 71.4 - - - +
246B GLN* 1.3 61.4 + - - +
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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