Contacts of the strand formed by residues 18 - 28 (chain A) in PDB entry 2DQM
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 TYR 18 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A PRO* 3.4 18.9 - - - +
17A ASP* 1.3 92.7 - - + +
19A GLN* 1.3 64.6 + - - +
42A ALA* 4.9 2.5 - - + -
43A VAL 3.5 6.3 - - - +
44A ARG* 3.1 54.8 + - + -
45A HIS* 4.4 0.4 - - - +
50A ALA 2.6 23.2 + - - -
51A PRO 3.4 23.3 - - - -
52A LEU* 3.7 35.7 - - + -
53A ARG 5.3 0.2 - - - -
86A LEU* 4.0 11.2 + - + +
90A PHE* 3.8 33.7 - + - -
132A LEU* 3.3 18.3 - - + +
137A VAL* 4.3 0.5 - - - +
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Residues in contact with GLN 19 (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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16A PRO* 3.5 21.6 - - + +
18A TYR* 1.3 75.6 - - - +
20A ILE* 1.3 67.3 + - - +
21A THR* 4.0 7.0 - - + -
41A GLN 4.1 0.2 - - - +
42A ALA* 3.3 5.4 - - - +
43A VAL* 2.9 34.5 + - + +
45A HIS* 3.6 33.9 - - + +
132A LEU* 4.3 0.9 - - - -
136A ASP 3.1 23.8 + - - -
137A VAL* 3.4 25.8 - - - +
138A LEU 3.8 6.3 + - - +
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Residues in contact with ILE 20 (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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19A GLN* 1.3 81.7 + - - +
21A THR* 1.3 60.3 + - - +
22A ASP 3.6 21.8 - - - +
40A SER* 3.7 25.4 - - - +
41A GLN 3.3 4.3 - - - +
42A ALA* 4.3 11.4 - - + -
52A LEU* 5.7 2.2 - - + -
54A LEU* 4.9 8.5 - - + -
92A LEU* 5.0 6.3 - - + -
131A TYR* 3.5 43.7 - - + +
132A LEU* 3.8 24.2 - - + +
137A VAL* 3.8 9.1 - - + +
138A LEU 3.3 11.1 - - - +
139A ALA* 3.2 18.6 - - + +
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Residues in contact with THR 21 (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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19A GLN* 5.1 6.3 - - + -
20A ILE* 1.3 76.2 - - - +
22A ASP* 1.3 84.2 + - - +
41A GLN* 3.0 17.3 + - - +
43A VAL* 4.2 25.5 - - + +
45A HIS* 6.3 0.2 - - - +
138A LEU 4.2 5.5 - - - +
139A ALA* 3.4 1.8 - - - -
140A ARG* 2.9 38.8 + - - +
181A PRO* 5.8 0.2 - - - +
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Residues in contact with ASP 22 (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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20A ILE* 3.6 4.9 - - - +
21A THR* 1.3 101.1 + - - +
23A ILE* 1.3 61.9 + - - +
39A VAL 3.9 0.6 - - - +
40A SER* 3.3 2.8 - - - -
41A GLN* 2.9 45.0 + - + +
139A ALA* 4.5 0.2 - - - -
140A ARG* 2.7 50.5 + - - +
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Residues in contact with ILE 23 (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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20A ILE* 4.6 0.2 - - + -
22A ASP* 1.3 76.3 - - - +
24A ASP* 1.3 65.2 + - - +
25A LEU* 3.9 31.6 + - + -
38A ALA* 4.2 7.9 - - + -
39A VAL 3.3 6.3 - - - +
40A SER* 3.5 15.7 - - - +
125A PHE* 4.5 6.5 - - + -
129A THR* 5.3 0.2 - - + -
131A TYR* 3.6 36.6 - - + +
139A ALA* 4.3 1.6 - - + -
140A ARG 3.0 6.3 + - - +
141A PHE* 3.6 42.6 - - + -
142A THR* 3.1 23.6 + - - +
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Residues in contact with ASP 24 (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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23A ILE* 1.3 71.9 - - - +
25A LEU* 1.3 68.1 + - - +
26A THR* 3.9 10.4 + - - -
37A THR 3.6 2.1 - - - +
38A ALA* 3.6 1.4 - - - -
39A VAL* 2.8 54.9 + - + +
142A THR* 3.5 27.2 - - - +
144A LYS* 5.6 0.5 - - - +
175A GLN* 4.0 10.5 + - - -
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Residues in contact with LEU 25 (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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23A ILE* 3.9 14.4 - - + -
24A ASP* 1.3 75.6 + - - +
26A THR* 1.3 60.3 + - - +
27A PHE* 3.9 13.5 - - + -
36A VAL* 4.1 18.4 - - + -
37A THR 3.5 0.9 - - - -
38A ALA* 3.6 27.8 - - + -
125A PHE* 4.0 21.5 - - + -
129A THR* 4.6 1.6 - - + -
141A PHE* 3.9 19.1 - - + -
142A THR 2.8 13.6 + - - +
143A THR* 3.5 4.4 - - + +
144A LYS* 2.7 31.6 + - - +
187A PHE* 3.7 32.8 - - + -
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Residues in contact with THR 26 (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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24A ASP* 3.9 9.9 + - - -
25A LEU* 1.3 78.3 + - - +
27A PHE* 1.3 66.5 + - - +
28A ASP* 5.0 1.8 - - + +
35A VAL 3.5 1.7 - - - +
36A VAL* 3.5 5.4 - - - +
37A THR* 2.9 49.9 + - - +
144A LYS* 3.3 23.7 + - + +
146A ILE* 3.9 27.1 - - + -
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Residues in contact with PHE 27 (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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25A LEU* 3.9 24.0 - - + -
26A THR* 1.3 78.5 - - - +
28A ASP* 1.3 60.6 - - - +
29A LEU* 3.3 20.5 + - + -
34A THR* 4.1 10.3 - - + -
35A VAL 3.6 1.6 - - - -
36A VAL* 3.9 21.5 - - + -
109A LEU* 4.5 9.6 - - + -
128A ILE* 3.7 31.6 - - + -
143A THR* 3.9 11.2 - - + -
144A LYS 2.8 12.1 + - - +
145A ILE* 4.5 1.8 - - - -
146A ILE* 2.8 31.0 + - - +
187A PHE* 3.7 34.8 - + - -
189A LEU* 3.6 23.3 - - + -
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Residues in contact with ASP 28 (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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26A THR* 4.1 1.9 - - + +
27A PHE* 1.3 70.3 - - - +
29A LEU* 1.3 62.0 + - - +
30A ASP* 5.9 0.5 - - - +
33A LYS 4.0 2.8 - - - +
34A THR* 3.4 5.1 - - - -
35A VAL* 2.9 49.9 + - + +
146A ILE* 3.8 13.9 - - + +
171A ARG* 3.2 37.8 + - - -
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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