Contacts of the strand formed by residues 26 - 36 (chain N) in PDB entry 1MMJ
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 TRP 26 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19N GLN* 3.6 20.4 - - - +
20N TYR* 3.0 29.2 - - - -
21N ARG* 3.1 33.7 - - + -
22N SER* 4.2 2.4 + - - -
25N SER* 1.3 94.8 + - - +
27N ALA* 1.3 64.5 + - - +
28N HIS 4.3 0.2 - - - -
52N THR* 3.5 31.0 - - + -
53N PHE 4.3 0.4 - - - -
54N ARG* 3.0 73.5 - - + +
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Residues in contact with ALA 27 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19N GLN* 3.7 4.7 - - - -
20N TYR* 2.8 66.0 + - + +
22N SER* 3.9 11.0 - - - +
26N TRP* 1.3 77.0 - - - +
28N HIS* 1.4 69.7 + - - +
29N THR 3.1 0.3 + - - -
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Residues in contact with HIS 28 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17N SER* 2.8 22.6 + - - -
19N GLN* 3.5 15.9 - - - +
20N TYR* 4.4 2.6 - - - -
26N TRP 4.3 0.2 - - - -
27N ALA* 1.4 75.2 - - - +
29N THR* 1.3 63.0 + - - +
30N CYS 2.9 30.1 + - - -
31N GLY* 4.1 1.6 - - - -
62N LEU* 3.8 27.9 - - + +
132N TRP* 3.5 37.8 - + + +
141N LEU* 4.6 25.1 - - + +
186N GLY* 3.1 29.2 + - - -
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Residues in contact with THR 29 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18N LEU* 2.7 25.2 + - - +
19N GLN* 4.5 0.3 - - - -
20N TYR* 3.4 32.7 - - + -
27N ALA 3.1 1.8 + - - -
28N HIS* 1.3 81.3 - - - +
30N CYS* 1.3 72.3 + - - +
49N ARG* 3.2 43.2 + - - +
51N LEU* 5.4 0.7 - - + -
53N PHE* 4.4 2.1 - - - -
186N GLY* 3.6 16.7 - - - -
241N FR1 3.9 5.2 - - - -
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Residues in contact with CYS 30 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18N LEU* 2.5 40.7 + - + -
28N HIS* 2.9 18.6 + - - -
29N THR* 1.3 97.3 + - - +
31N GLY* 1.3 61.9 - - - +
46N CYS* 2.0 55.9 - - + -
49N ARG* 4.5 1.1 - - - -
186N GLY 3.8 4.0 - - - -
188N SER 3.0 7.9 - - - +
241N FR1 3.7 15.3 - - - -
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Residues in contact with GLY 31 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15N GLN* 3.9 9.4 - - - -
16N ILE* 3.3 15.9 - - - -
18N LEU* 4.0 4.2 - - - +
28N HIS* 4.4 3.6 - - - -
30N CYS* 1.3 81.4 - - - +
32N GLY* 1.3 52.6 + - - -
42N THR* 2.8 26.7 + - - -
131N GLY* 6.3 1.6 - - - -
186N GLY 4.0 4.7 + - - -
187N ASP* 4.7 2.2 - - - -
188N SER 2.9 8.9 + - - -
189N GLY 3.5 9.3 - - - +
190N GLY* 4.0 6.5 - - - -
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Residues in contact with GLY 32 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14N SER 3.8 0.9 - - - +
15N GLN* 3.8 3.8 - - - -
16N ILE* 3.0 40.4 + - - +
31N GLY* 1.3 75.0 - - - -
33N THR* 1.4 65.1 + - - -
40N VAL* 4.4 0.4 - - - -
41N MET 3.2 13.7 - - - -
42N THR* 4.1 3.4 - - - -
189N GLY 3.4 7.9 + - - -
190N GLY* 3.8 1.4 - - - -
191N PRO* 4.0 8.2 - - - +
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Residues in contact with THR 33 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14N SER* 3.3 23.3 - - - +
16N ILE* 4.2 0.4 - - - +
32N GLY* 1.4 76.7 - - - -
34N LEU* 1.4 77.6 + - - +
35N ILE* 3.2 10.3 + - + +
40N VAL* 4.2 3.1 - - - -
41N MET* 2.8 47.5 + - + +
112N GLY* 3.9 9.0 - - - -
114N LEU* 4.9 0.2 - - + -
189N GLY 5.2 0.3 + - - -
190N GLY 4.7 0.7 - - - -
191N PRO* 3.4 26.5 - - - +
202N VAL* 4.0 16.3 - - + +
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Residues in contact with LEU 34 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13N PRO 5.1 0.7 - - - +
14N SER* 2.8 18.5 + - - +
16N ILE* 4.0 10.4 - - + +
33N THR* 1.4 69.7 - - - +
35N ILE* 1.3 53.0 + - - +
36N ARG 3.1 23.6 - - - +
37N GLN* 4.7 3.1 - - - -
39N TRP 3.8 6.5 - - - +
40N VAL* 4.4 11.2 - - + -
57N VAL* 4.6 13.0 - - + -
99N LEU* 4.8 6.3 - - + -
103N VAL* 4.0 10.3 - - + -
105N LEU* 4.4 1.1 - - + -
109N VAL* 3.5 32.3 - - + -
110N GLN 3.9 15.3 - - - +
111N LEU* 3.8 17.0 - - + -
112N GLY* 2.6 34.9 + - - -
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Residues in contact with ILE 35 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33N THR* 3.2 15.0 + - + +
34N LEU* 1.3 75.3 - - - +
36N ARG* 1.3 91.7 + - - +
39N TRP* 3.1 19.3 + - + +
40N VAL* 4.3 0.4 - - - -
41N MET* 3.8 23.1 - - + +
96N LEU* 4.2 13.9 - - + -
111N LEU* 3.9 13.0 - - - +
112N GLY 4.3 7.9 - - - +
114N LEU* 3.7 33.7 - - + -
233N ILE* 3.6 31.6 - - + -
237N ILE* 3.7 15.5 - - + -
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Residues in contact with ARG 36 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34N LEU* 3.1 12.3 - - - +
35N ILE* 1.3 99.9 + - - +
37N GLN* 1.4 62.0 + - - +
38N ASN* 2.9 23.5 + - - +
39N TRP* 2.9 26.2 + - + +
111N LEU* 3.9 20.2 - - - +
114N LEU* 6.2 2.0 - - - +
233N ILE* 4.7 4.2 - - - +
234N ASN* 3.9 20.8 - - - +
237N ILE* 3.5 45.0 - - + +
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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