Contacts of the strand formed by residues 25 - 32 (chain B) in PDB entry 3DM6
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 GLN 25 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B MET 3.6 0.5 - - - +
19B THR* 3.1 5.9 - - - -
20B VAL* 2.8 45.3 + - + +
23B PRO 4.1 6.4 + - - +
24B PRO* 1.3 75.5 - - - +
26B THR* 1.3 64.8 + - - +
27B LEU* 3.6 4.3 + - + +
51B TYR 3.9 4.8 - - - +
52B TYR* 3.6 25.8 - - - -
53B GLN* 2.9 49.4 + - - +
56B LEU* 4.7 7.5 + - + +
57B SER* 4.2 13.5 - - - +
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Residues in contact with THR 26 (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 GLU* 4.0 28.3 + - + +
18B MET 3.4 4.0 - - - -
19B THR* 3.3 17.7 - - - +
24B PRO 4.2 0.6 + - - -
25B GLN* 1.3 71.4 - - - +
27B LEU* 1.3 63.7 + - - +
50B ARG* 2.3 55.8 + - - +
88B PRO* 5.4 0.2 - - - +
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Residues in contact with LEU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B GLU* 3.6 2.3 - - - +
18B MET* 2.7 41.2 + - + +
20B VAL* 3.7 28.0 - - + -
25B GLN* 3.6 4.7 + - + +
26B THR* 1.3 80.3 - - - +
28B ASN* 1.3 65.7 + - - +
29B ILE* 3.8 11.6 + - + -
40B VAL* 4.5 15.7 - - + -
41B GLY 5.1 0.4 - - - +
50B ARG* 3.8 17.3 - - + +
51B TYR* 3.9 15.5 - - - +
52B TYR* 4.1 21.5 - - + +
116B GLU* 3.3 35.0 - - + +
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Residues in contact with ASN 28 (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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7B ARG* 3.7 8.6 + - - +
15B TYR* 3.1 31.6 - - + -
16B VAL 3.6 1.6 - - - -
17B GLU* 3.4 28.7 + - - +
27B LEU* 1.3 72.3 - - - +
29B ILE* 1.3 61.8 + - - +
50B ARG* 3.4 20.0 + - - +
114B ASN* 3.0 38.4 + - - +
115B TRP* 3.6 4.6 - - - -
116B GLU* 2.8 37.0 + - - +
117B GLY 3.3 5.4 + - - -
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Residues in contact with ILE 29 (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 TYR* 3.1 4.4 - - - +
16B VAL* 2.6 43.1 + - + +
18B MET* 3.5 37.9 - - + -
27B LEU* 4.2 11.2 - - + +
28B ASN* 1.3 78.6 - - - +
30B LEU* 1.3 61.8 + - - +
31B VAL 3.3 1.0 + - - -
38B PHE* 4.1 4.9 - - + -
40B VAL* 3.9 20.4 - - + -
116B GLU 4.6 0.2 - - - -
117B GLY* 3.4 26.2 - - - +
118B ILE 3.4 6.7 - - - +
119B LEU* 3.2 42.6 - - + +
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Residues in contact with LEU 30 (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 GLY* 3.4 34.8 - - - -
14B TYR 3.2 15.3 - - - +
15B TYR* 3.7 4.6 - - - +
28B ASN 4.1 0.4 + - - -
29B ILE* 1.3 69.3 - - - +
31B VAL* 1.3 64.6 + - - +
32B ASP* 3.4 5.5 + - + -
115B TRP* 3.8 24.8 - - + +
117B GLY 3.0 16.2 + - - +
118B ILE* 3.6 28.0 - - + +
119B LEU* 2.7 31.7 + - - -
229B SER 5.7 0.2 - - - +
230B GLY* 5.1 3.8 - - - -
1000B 757 3.7 36.6 - - + +
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Residues in contact with VAL 31 (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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6B LEU* 3.8 29.8 - - + -
14B TYR* 2.8 23.2 + - + +
16B VAL* 4.1 7.6 - - + -
29B ILE 4.0 9.9 - - - +
30B LEU* 1.3 73.2 - - - +
32B ASP* 1.3 56.7 + - - +
119B LEU* 4.2 7.2 - - + -
121B LEU* 3.8 16.6 - - + -
152B LEU* 3.6 28.7 - - + -
154B LEU* 5.7 0.9 - - + -
174B MET* 4.0 14.8 - - - -
229B SER* 2.7 36.9 + - - +
230B GLY* 4.0 1.2 + - - -
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Residues in contact with ASP 32 (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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30B LEU* 3.4 3.3 + - + +
31B VAL* 1.3 76.1 - - - +
33B THR* 1.3 60.1 + - - +
34B GLY 3.0 3.1 + - - -
35B SER* 2.4 25.2 + - - +
118B ILE* 3.5 19.6 - - + +
119B LEU 2.8 16.2 + - - +
120B GLY* 3.3 3.8 - - - -
121B LEU* 2.9 22.4 + - - -
228B ASP* 2.7 27.7 - - - +
229B SER* 3.4 1.6 - - - -
230B GLY* 3.3 7.6 - - - +
1000B 757 2.8 34.6 + - - +
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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