Contacts of the strand formed by residues 39 - 52 (chain B) in PDB entry 5JTP
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 GLU 39 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36B TRP* 5.4 1.6 - - - +
37B GLN 3.6 2.2 + - - -
38B PRO* 1.4 68.9 - - - +
40B VAL* 1.3 83.1 + - - +
41B LYS* 3.8 2.4 + - + +
65B THR 3.3 2.4 - - - +
66B ALA* 3.2 20.3 - - - -
67B SER* 3.1 23.9 + - - +
69B GLY 6.0 0.9 - - - +
467F ALA* 5.1 10.4 - - - +
470F LEU* 3.8 14.6 - - - +
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Residues in contact with VAL 40 (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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38B PRO 3.6 13.0 - - - +
39B GLU* 1.3 89.5 + - - +
41B LYS* 1.3 67.0 + - - +
42B LEU* 4.8 5.6 - - + +
64B VAL* 4.0 21.8 - - + -
65B THR 3.6 4.0 - - - -
66B ALA* 4.9 1.3 - - + +
126B LEU* 3.8 20.9 - - + -
128B LEU* 5.6 7.2 - - + -
467F ALA* 6.1 1.2 - - - +
468F LEU* 3.8 23.3 - - + +
470F LEU* 3.8 25.5 - - + +
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Residues in contact with LYS 41 (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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39B GLU* 4.8 2.5 - - + +
40B VAL* 1.3 77.7 - - - +
42B LEU* 1.3 67.3 + - - +
43B ASP* 2.8 37.7 + - - +
63B THR 3.7 0.5 - - - +
64B VAL* 3.6 3.5 - - - -
65B THR* 2.8 54.6 + - + +
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Residues in contact with LEU 42 (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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40B VAL* 4.3 6.4 - - + +
41B LYS* 1.3 85.0 + - - +
43B ASP* 1.3 77.7 + - - +
44B LEU* 5.3 5.2 - - + -
62B VAL* 3.6 30.1 - - + -
63B THR 3.7 4.3 - - - +
64B VAL* 4.3 8.1 - - + +
128B LEU* 3.6 36.3 - - + -
131B VAL* 4.9 11.4 - - + -
462F TYR* 3.3 37.0 + - + -
464F MET* 6.4 1.1 - - + -
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Residues in contact with ASP 43 (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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41B LYS* 2.8 38.1 + - - +
42B LEU* 1.3 80.8 - - - +
44B LEU* 1.3 62.2 + - - +
45B ASP* 5.1 6.5 - - - +
62B VAL* 3.5 5.0 - - - +
63B THR* 2.8 53.4 + - - +
65B THR* 4.1 9.5 + - - -
462F TYR* 3.1 8.7 + - - -
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Residues in contact with LEU 44 (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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42B LEU* 5.3 6.3 - - + -
43B ASP* 1.3 76.7 - - - +
45B ASP* 1.3 79.7 + - - +
46B THR* 3.8 15.3 - - + -
60B LEU* 3.7 16.8 - - + -
61B ARG 3.3 11.0 - - - +
62B VAL* 3.8 17.5 - - + -
107B PHE* 5.2 5.2 - - + -
128B LEU* 5.7 0.2 - - + -
131B VAL* 6.2 2.0 - - + -
133B PHE* 3.7 35.2 - - + -
458F THR 4.0 1.7 - - - +
460F LEU* 3.5 21.0 + - + +
462F TYR* 3.3 37.3 + - + -
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Residues in contact with ASP 45 (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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43B ASP* 5.1 4.2 - - - +
44B LEU* 1.3 80.1 + - - +
46B THR* 1.3 68.7 + - - +
47B ALA 4.4 0.2 - - - -
61B ARG* 2.9 71.6 + - + +
63B THR* 5.0 3.3 + - - -
458F THR* 3.1 35.0 - - + +
460F LEU* 3.6 5.4 - - - -
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Residues in contact with THR 46 (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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44B LEU* 3.8 17.9 - - + -
45B ASP* 1.3 80.5 - - - +
47B ALA* 1.3 60.1 + - - +
59B VAL 3.5 7.2 - - - +
60B LEU* 4.7 2.9 - - - -
98B LEU 5.2 0.7 - - - -
99B GLY 5.1 1.1 - - - +
103B PRO* 3.6 34.3 - - + -
133B PHE* 5.3 1.1 - - + -
456F ASP* 4.0 5.0 - - - +
457F GLN* 2.8 67.2 + - - +
458F THR* 4.1 2.0 + - - +
460F LEU* 3.3 20.4 - - + +
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Residues in contact with ALA 47 (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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46B THR* 1.3 73.6 - - - +
48B SER* 1.3 62.1 + - - +
58B VAL* 3.3 11.8 - - - +
59B VAL* 2.8 46.4 + - + +
98B LEU 5.0 1.5 - - - +
456F ASP* 3.5 17.3 - - - +
457F GLN* 5.7 1.3 - - - +
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Residues in contact with SER 48 (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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47B ALA* 1.3 77.4 - - - +
49B SER* 1.3 65.9 + - - +
56B TYR* 5.5 1.1 - - - -
57B GLU 3.2 11.0 - - - -
58B VAL* 3.9 19.3 - - - +
59B VAL* 5.4 0.9 - - - -
98B LEU* 4.5 22.4 - - - +
454F LEU* 5.0 9.5 + - - +
456F ASP* 2.9 23.1 + - - +
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Residues in contact with SER 49 (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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29A PRO* 5.4 0.2 - - - +
48B SER* 1.3 75.8 - - - +
50B GLN* 1.3 60.1 + - - +
51B LEU* 3.7 10.6 - - - +
56B TYR* 3.2 14.3 - - - +
57B GLU* 2.9 55.8 + - - +
59B VAL* 6.2 0.2 - - - -
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Residues in contact with GLN 50 (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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49B SER* 1.3 74.1 - - - +
51B LEU* 1.3 66.1 + - - +
52B ALA 2.7 28.4 + - - +
54B ASP 4.0 2.8 - - - +
55B VAL 2.9 20.2 + - - +
56B TYR* 3.1 25.3 - - + -
450F ASN* 2.7 51.4 + - - +
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Residues in contact with LEU 51 (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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29A PRO* 3.6 39.5 - - + +
30A HIS* 5.3 5.6 - - + -
32A PHE* 5.8 0.4 - - + -
33A GLN* 3.7 31.9 + - + +
49B SER* 3.7 20.6 - - - +
50B GLN* 1.3 78.1 - - - +
52B ALA* 1.3 62.6 + - - +
55B VAL* 3.2 28.0 + - + +
57B GLU* 3.7 19.7 - - + -
83B ILE* 3.8 15.7 - - + -
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Residues in contact with ALA 52 (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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33A GLN* 4.3 11.2 - - - +
50B GLN* 2.7 30.5 + - - -
51B LEU* 1.3 78.0 - - + +
53B ASP* 1.3 57.5 + - - +
55B VAL* 2.9 25.9 + - + +
450F ASN* 4.5 2.5 - - - -
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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