Contacts of the strand formed by residues 236 - 246 (chain A) in PDB entry 1Q90
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 236 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A HIS* 5.7 0.9 - - - -
27A ALA* 3.4 15.9 - - - +
29A LYS* 3.7 15.2 - - - +
153A ASN* 3.2 14.9 + - - +
154A ARG* 2.9 36.6 + - - +
235A GLY* 1.3 75.0 - - - -
237A PHE* 1.3 60.4 + - - -
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Residues in contact with PHE 237 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A ILE* 3.5 32.3 - - + -
21A CYS* 3.9 14.8 - - + -
22A ALA* 3.5 39.9 - - + -
25A HIS* 4.0 20.6 - - + +
27A ALA 3.3 15.2 + - - +
28A GLN* 3.2 12.3 - - - +
29A LYS 2.9 17.8 + - - -
151A GLY* 3.6 4.5 - - - -
152A GLY 2.8 48.9 - - - -
153A ASN* 4.0 7.2 - - + -
236A GLY* 1.3 74.5 - - - -
238A GLY* 1.3 63.6 + - - +
239A GLN* 3.8 23.8 - - + -
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Residues in contact with GLY 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A GLN* 5.6 1.8 - - - -
29A LYS 3.2 18.0 + - - -
30A ALA* 5.2 0.7 - - - -
31A VAL* 3.4 14.2 - - - +
151A GLY 3.7 0.2 - - - -
152A GLY 2.7 38.0 + - - +
237A PHE* 1.3 80.0 - - - +
239A GLN* 1.3 64.6 - - - -
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Residues in contact with GLN 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A GLY 2.9 23.2 + - - -
18A ARG* 3.1 12.7 - - - +
19A ILE* 2.3 42.1 + - + +
22A ALA* 5.2 0.3 - - - +
31A VAL* 3.4 8.2 + - - +
150A PHE 3.4 7.4 - - - +
237A PHE* 3.8 23.0 - - + -
238A GLY* 1.3 75.1 - - - -
240A ALA* 1.3 67.4 + - - +
73D LEU* 5.0 5.4 - - - +
74D GLU* 5.8 3.1 - - - +
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Residues in contact with ALA 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A VAL* 3.7 22.7 - - + +
32A GLU* 5.1 0.9 - - - -
33A ILE* 4.3 19.3 - - + +
149A TYR* 3.7 2.8 - - - +
150A PHE* 2.9 33.0 + - + +
239A GLN* 1.3 82.6 + - - +
241A GLU* 1.3 62.8 + - - +
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Residues in contact with GLU 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ARG* 4.7 4.7 + - - -
33A ILE* 4.7 3.0 - - - +
147A PRO* 4.6 6.1 - - - +
148A ILE 3.4 6.1 - - - +
149A TYR* 3.6 37.4 + - + -
240A ALA* 1.3 77.8 - - - +
242A THR* 1.3 74.6 + - - +
243A GLU* 5.8 2.4 - - + +
74D GLU* 5.6 2.5 - - - +
1G MET* 3.9 28.1 - - - +
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Residues in contact with THR 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ILE* 3.9 28.8 + - + +
34A GLU* 5.6 0.3 - - - -
35A VAL* 4.3 12.3 + - + +
147A PRO* 3.2 6.8 - - - +
148A ILE* 2.7 58.3 + - + +
241A GLU* 1.3 82.1 - - - +
243A GLU* 1.3 77.2 + - - +
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Residues in contact with GLU 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A VAL* 3.5 13.8 - - - +
36A PRO 4.2 3.1 - - - +
37A GLN* 4.9 1.7 - - - +
145A LYS* 3.1 45.3 + - + +
146A TYR 2.9 13.0 - - - +
147A PRO* 4.0 6.7 - - + -
148A ILE* 4.5 2.5 - - - +
241A GLU* 5.8 2.5 - - + +
242A THR* 1.3 95.6 + - - +
244A ILE* 1.3 62.2 + - - +
61D ALA* 4.2 8.5 - - + +
1G MET* 4.8 15.8 - - - +
3G GLU* 5.2 6.6 - - - +
4G PRO* 5.8 5.4 - - - +
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Residues in contact with ILE 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A VAL* 3.5 14.8 - - + -
36A PRO* 2.8 47.1 - - + +
37A GLN 4.0 2.9 - - - -
38A ALA 4.4 5.2 - - - +
39A VAL* 4.2 19.1 - - + -
45A PHE* 4.3 12.3 - - + -
78A PRO* 4.7 0.7 - - + -
81A PHE* 4.2 19.3 - - + -
145A LYS* 3.5 0.8 - - - -
146A TYR* 2.7 53.8 + - + +
148A ILE* 3.9 20.2 - - + -
243A GLU* 1.3 74.4 - - - +
245A VAL* 1.3 64.1 + - - +
246A LEU 3.8 1.0 + - - -
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Residues in contact with VAL 245 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A GLN* 3.1 37.5 + - - +
38A ALA* 3.0 6.3 - - + -
39A VAL 2.7 31.5 + - - -
143A TYR 6.1 0.2 - - - -
144A LEU 3.7 7.6 - - - +
145A LYS* 4.0 24.7 - - + -
244A ILE* 1.3 77.2 - - - +
246A LEU* 1.3 62.7 + - - +
247A GLN* 3.0 26.6 + - + -
57D LEU 4.1 5.6 - - - +
59D PRO* 3.9 24.5 - - + -
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Residues in contact with LEU 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A VAL* 3.3 26.2 - - + +
40A LEU 4.1 2.2 - - - +
41A PRO* 4.0 24.9 - - + -
81A PHE* 4.3 6.5 - - + -
132A SER* 4.1 6.7 - - - -
133A PRO* 3.9 16.2 - - + +
135A PRO* 4.5 7.4 - - + -
141A VAL* 3.8 30.3 - - + -
142A SER 3.9 9.6 - - - +
143A TYR* 3.4 32.5 - - + +
144A LEU 3.0 19.9 + - - +
146A TYR* 4.2 13.9 - - + -
244A ILE* 3.8 2.6 + - - +
245A VAL* 1.3 73.7 - - - +
247A GLN* 1.3 57.5 + - - +
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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