Contacts of the strand formed by residues 14 - 23 (chain B) in PDB entry 2W27
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 VAL 14 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7B ILE* 4.2 9.9 - - + -
11B ILE* 3.4 22.3 + - + +
12B ASP 3.3 5.6 - - - +
13B ASP* 1.3 79.8 - - - +
15B LEU* 1.3 63.7 + - - +
37B ARG 3.4 9.4 - - - +
38B ILE* 3.8 29.6 - - + +
47B LEU* 3.8 9.6 - - + -
64B VAL* 4.2 9.6 - - + +
67B ARG* 5.4 3.8 - - + -
68B ILE* 3.3 38.6 - - + +
71B GLN* 3.1 25.3 + - - +
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Residues in contact with LEU 15 (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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13B ASP 3.5 15.0 - - - +
14B VAL* 1.3 77.9 - - - +
16B PRO* 1.3 74.0 - - + +
17B TYR* 3.9 26.2 - - + -
36B GLY* 4.3 0.7 - - - -
37B ARG* 2.7 63.9 + - + +
38B ILE 4.0 0.9 - - - -
39B LEU* 3.9 15.7 - - + +
44B ILE* 4.5 9.4 - - + -
68B ILE* 4.6 2.5 - - - -
71B GLN* 3.5 4.5 - - - +
238B GLU* 4.0 16.8 - - + +
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Residues in contact with PRO 16 (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* 1.3 92.3 - - + +
17B TYR* 1.3 72.5 + - - +
18B TYR* 3.5 34.0 - - + +
34B VAL* 4.1 2.2 - - + -
35B LEU 3.4 9.0 - - - +
68B ILE* 3.9 20.4 - - + +
71B GLN* 3.4 23.8 - - + +
72B ALA* 3.8 22.9 - - + +
238B GLU* 4.4 4.3 - - - +
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Residues in contact with TYR 17 (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* 3.8 9.2 + - + -
16B PRO* 1.3 79.4 - - - +
18B TYR* 1.3 67.1 + - - +
34B VAL* 4.0 0.5 - - - -
35B LEU* 3.0 32.2 + - + +
37B ARG* 3.8 34.3 - - + +
44B ILE* 3.0 41.9 - - + +
236B PRO* 3.7 17.0 - - + -
237B SER* 3.4 32.3 - - - +
238B GLU* 3.3 32.9 - - + +
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Residues in contact with TYR 18 (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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16B PRO* 3.5 30.9 - - + +
17B TYR* 1.3 77.7 - - - +
19B GLN* 1.3 60.5 + - - +
20B ALA 4.2 0.7 + - - -
32B TYR* 3.7 26.1 - - + -
33B GLU 3.5 4.3 - - - -
34B VAL* 4.4 12.1 - - + -
71B GLN 4.1 0.5 + - - -
72B ALA* 3.6 21.4 - - + -
75B ARG* 3.2 28.2 - - + +
76B PHE* 4.2 11.0 - + - -
235B SER 4.3 0.7 - - - +
236B PRO* 3.2 4.6 - - - +
237B SER* 2.8 37.3 + - - +
238B GLU 3.4 28.3 - - - -
239B THR* 4.3 2.0 - - - +
240B PHE* 3.7 35.7 - + + -
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Residues in contact with GLN 19 (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 TYR* 1.3 73.3 - - - +
20B ALA* 1.3 71.6 + - - +
21B ILE* 4.1 1.9 - - - +
32B TYR* 3.2 4.7 - - - -
33B GLU* 2.8 37.8 + - - +
35B LEU* 4.0 14.1 - - + +
229B GLN* 3.4 25.7 + - - +
230B GLY 2.9 33.9 + - - +
231B TYR 3.7 0.4 - - - +
234B VAL 2.7 28.4 + - - +
235B SER* 4.3 2.7 - - - +
236B PRO* 4.0 13.8 - - + +
501B 5GP 2.7 33.3 + - - -
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Residues in contact with ALA 20 (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 TYR 4.2 0.4 + - - -
19B GLN* 1.3 87.3 + - - +
21B ILE* 1.3 62.1 + - - +
22B PHE* 3.7 31.8 - - + -
29B VAL* 3.9 15.0 - - + -
31B GLY 3.6 1.1 - - - -
32B TYR* 3.5 28.5 - - + -
228B PHE 4.2 0.7 - - - +
229B GLN* 4.1 7.4 - - - +
230B GLY 5.2 0.2 + - - -
233B LEU* 5.6 0.3 - - - +
234B VAL* 4.9 6.3 + - + +
241B LEU* 4.5 11.2 - - + -
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Residues in contact with ILE 21 (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 GLN 4.1 5.6 - - - +
20B ALA* 1.3 76.9 - - - +
22B PHE* 1.3 65.1 + - - +
29B VAL* 3.4 4.9 - - - -
30B VAL* 2.9 38.8 + - + -
31B GLY 3.0 11.9 + - - +
33B GLU* 4.5 6.3 - - + +
86B PHE* 3.3 45.3 - - + -
173B LYS* 5.0 0.4 - - - +
207B LEU* 3.9 12.1 - - + -
227B TYR* 3.8 24.7 - - + -
228B PHE 3.4 12.8 - - - +
229B GLN* 3.8 27.6 - - - +
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Residues in contact with PHE 22 (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 ALA* 3.7 31.9 - - + -
21B ILE* 1.3 75.6 - - - +
23B SER* 1.3 61.4 + - - +
27B GLN 4.8 0.2 - - - -
28B LYS* 3.4 19.3 - - - +
29B VAL* 3.7 16.8 - - + -
30B VAL* 4.9 0.2 - - - -
227B TYR* 3.4 6.9 - - - -
228B PHE* 2.9 40.9 + - + +
233B LEU* 3.7 34.3 - - + -
234B VAL* 3.8 15.9 - - + -
241B LEU* 5.2 1.8 - - + -
243B ARG 5.3 0.2 - - - -
245B VAL* 5.4 1.3 - - + -
246B LEU* 3.3 35.7 - - + -
250B LEU* 3.9 29.8 - - + -
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Residues in contact with SER 23 (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 ILE 4.3 0.4 + - - -
22B PHE* 1.3 74.8 - - - +
24B ALA* 1.3 59.2 + - - +
25B GLU* 4.0 13.5 - - - -
26B GLU* 3.4 20.3 + - - +
27B GLN* 3.0 22.9 + - - -
28B LYS* 3.0 24.7 + - - +
30B VAL* 4.6 9.8 - - - +
226B ARG 3.7 5.6 - - - -
227B TYR* 4.1 18.1 - - - -
228B PHE* 4.4 1.9 - - - -
250B LEU* 5.0 0.5 - - - +
254B PHE* 4.5 2.3 - - - -
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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