Contacts of the strand formed by residues 24 - 30 (chain T) in PDB entry 2JA7
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 CYS 24 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15T VAL* 3.7 24.5 - - + -
16T ASP 3.2 9.9 - - - +
17T PRO* 3.3 32.5 - - - -
20T TYR 5.0 1.6 - - - -
23T VAL* 1.3 82.4 - - - +
25T ARG* 1.3 62.0 + - - +
26T ILE* 3.9 2.3 + - + +
42T ILE* 2.8 33.3 + - - +
44T VAL* 3.4 28.1 - - + +
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Residues in contact with ARG 25 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537M ARG* 2.8 38.2 - - - +
598M LEU* 2.9 44.3 + - - +
599M SER 3.4 1.8 + - - -
600M PRO* 3.2 26.6 - - - +
14T GLU 4.1 1.2 - - - +
15T VAL* 4.0 0.5 - - - -
16T ASP* 3.0 42.4 + - + +
24T CYS* 1.3 73.0 - - - +
26T ILE* 1.3 69.4 + - - +
27T GLU* 5.2 5.6 - - + +
39T THR* 4.2 17.6 - - + +
40T LEU 4.3 4.5 - - - +
41T ASP* 2.7 32.1 + - - +
122T LEU* 4.1 0.4 - - - +
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Residues in contact with ILE 26 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12T VAL* 4.1 17.3 - - + -
14T GLU 3.9 1.1 - - - -
15T VAL* 3.6 26.7 - - + -
24T CYS 3.9 4.0 + - - +
25T ARG* 1.3 77.2 - - - +
27T GLU* 1.3 78.0 + - - +
28T ALA* 4.4 4.0 - - + +
38T LEU* 5.5 4.2 - - + +
39T THR* 3.2 4.5 - - - +
40T LEU* 2.7 48.8 + - + +
42T ILE* 4.8 19.5 - - + -
44T VAL* 5.6 1.8 - - + -
49T VAL* 3.1 44.6 - - + -
55T LEU* 5.0 6.5 - - + -
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Residues in contact with GLU 27 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12T VAL* 3.6 1.0 - - - -
13T SER* 2.7 47.8 + - - +
14T GLU* 3.5 21.9 + - - +
25T ARG* 5.2 6.7 - - + +
26T ILE* 1.3 85.9 - - - +
28T ALA* 1.3 54.6 + - - +
38T LEU 3.2 7.4 - - - +
39T THR* 3.7 28.0 + - + +
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Residues in contact with ALA 28 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10T PHE* 3.8 14.4 - - + -
11T GLN 2.8 37.2 - - - +
12T VAL* 3.5 10.1 - - + +
13T SER* 3.9 4.0 - - - +
26T ILE* 4.4 5.0 - - + +
27T GLU* 1.3 74.1 - - - +
29T ALA* 1.3 58.8 + - - +
37T LYS* 3.8 3.6 - - - +
38T LEU* 3.0 36.6 + - + +
55T LEU* 5.9 1.6 - - + -
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Residues in contact with ALA 29 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10T PHE* 2.9 30.3 - - - -
11T GLN* 3.0 15.1 + - + +
13T SER* 5.6 1.8 - - - -
28T ALA* 1.3 74.8 - - - +
30T SER* 1.3 65.5 + - - +
31T THR* 4.9 0.3 + - - -
36T CYS 4.0 6.7 - - - +
37T LYS* 4.7 6.3 - - + +
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Residues in contact with SER 30 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8T ASP* 2.8 31.2 + - - -
9T ILE 3.6 4.5 - - - -
10T PHE* 4.1 2.0 - - - -
29T ALA* 1.3 77.9 - - - +
31T THR* 1.3 58.2 + - - +
32T THR* 3.1 17.9 + - - +
33T GLN* 3.7 15.8 + - - +
34T ASP* 5.2 4.2 - - - +
36T CYS* 3.1 38.6 + - - +
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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