Contacts of the strand formed by residues 39 - 52 (chain B) in PDB entry 5JTO
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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37B GLN 4.1 0.8 + - - -
38B PRO* 1.3 67.0 - - - +
40B VAL* 1.3 66.2 + - - +
41B LYS* 5.0 3.9 - - + +
65B THR* 3.5 1.9 - - - +
66B ALA* 3.3 19.1 - - - -
67B SER* 2.9 30.9 + - - +
290H TRP* 5.8 0.9 - - + +
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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* 3.1 26.7 + - + +
39B GLU* 1.3 77.4 - - - +
41B LYS* 1.3 65.5 + - - +
42B LEU* 4.8 3.6 - - + -
64B VAL* 3.9 24.9 - - + -
65B THR 3.2 3.8 - - - -
66B ALA* 4.4 6.7 - - + +
74B PHE* 5.2 3.4 - - + -
126B LEU* 4.6 8.5 - - + -
290H TRP* 2.9 61.9 - - + +
296H THR* 3.8 22.4 - - - +
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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* 5.0 5.6 - - + +
40B VAL* 1.3 75.9 - - - +
42B LEU* 1.3 67.7 + - - +
43B ASP* 3.7 28.3 + - - +
63B THR* 3.4 2.2 - - - +
64B VAL* 3.3 9.0 - - - +
65B THR* 2.8 53.3 + - + +
287H PRO* 6.0 1.0 - - - +
290H TRP* 4.7 2.9 - - - -
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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
----------------------------------------------------------
40B VAL* 4.8 4.7 - - + -
41B LYS* 1.3 86.0 + - - +
43B ASP* 1.3 63.7 + - - +
44B LEU* 4.7 4.7 - - + -
62B VAL* 5.3 2.0 - - + -
63B THR 3.5 3.1 - - - +
64B VAL* 4.2 20.0 - - + -
128B LEU* 3.6 47.6 - - + -
287H PRO* 4.5 4.7 - - - +
288H VAL* 3.4 53.2 + - + +
289H ARG 4.7 0.2 - - - +
290H TRP* 3.7 36.3 - - + +
291H LEU* 5.1 1.3 - - + +
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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* 3.7 20.9 + - - +
42B LEU* 1.3 77.2 - - - +
44B LEU* 1.3 66.7 + - - +
45B ASP* 4.1 4.2 + - - +
61B ARG* 3.9 1.9 - - - +
63B THR* 3.0 48.4 + - + +
285H ASN* 3.0 29.8 + - - -
287H PRO* 3.5 20.2 - - + +
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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
----------------------------------------------------------
42B LEU* 4.7 5.4 - - + -
43B ASP* 1.3 84.4 + - - +
45B ASP* 1.3 60.5 + - - +
46B THR* 5.6 1.3 - - + -
60B LEU* 3.9 26.9 - - + -
61B ARG 3.1 12.8 - - - +
62B VAL* 4.3 21.5 - - + -
103B PRO* 6.3 0.4 - - + -
107B PHE* 5.3 2.7 - - + -
128B LEU* 5.7 3.4 - - + -
133B PHE* 3.7 33.9 - - + -
285H ASN* 3.4 5.6 - - - +
286H MET* 2.9 54.4 + - + +
288H VAL* 3.8 23.3 - - + -
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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
----------------------------------------------------------
43B ASP* 4.1 4.9 + - - +
44B LEU* 1.3 74.5 - - - +
46B THR* 1.3 74.3 + - - +
47B ALA* 4.0 6.2 + - - +
59B VAL 3.9 3.1 - - - +
60B LEU* 4.1 4.6 - - - +
61B ARG* 3.0 77.4 + - - +
285H ASN* 3.9 19.0 + - + +
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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* 5.5 1.3 - - + +
45B ASP* 1.3 85.7 + - - +
47B ALA* 1.3 60.9 + - - +
59B VAL 4.1 3.6 - - - -
60B LEU* 4.4 12.3 - - + -
103B PRO* 6.1 0.2 - - + -
281H PHE* 3.7 46.9 + - + +
282H ALA* 3.5 17.4 - - - +
284H GLY 3.5 22.6 + - - +
285H ASN* 4.7 4.7 - - - +
286H MET* 5.4 10.8 - - + +
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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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45B ASP* 4.0 10.0 + - - +
46B THR* 1.3 74.3 - - - +
48B SER* 1.3 61.6 + - - +
59B VAL* 2.9 54.6 + - + +
61B ARG* 5.6 2.0 - - - +
79B GLN* 5.5 4.3 - - - +
281H PHE* 3.5 5.9 - - - -
282H ALA* 4.6 2.5 - - - -
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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 75.8 - - - +
49B SER* 1.3 63.6 + - - +
56B TYR* 6.5 0.7 - - - -
57B GLU* 3.3 12.6 - - - -
58B VAL* 4.7 6.3 - - - -
59B VAL* 5.4 1.3 - - - -
278H LEU* 4.0 29.0 - - - +
281H PHE* 3.5 26.3 - - - +
282H ALA* 4.0 11.8 - - - +
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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* 5.5 1.0 - - - +
19B LYS* 5.2 1.2 + - - -
48B SER* 1.3 79.5 - - - +
50B GLN* 1.3 61.0 + - - +
51B LEU* 3.9 9.1 - - - +
56B TYR* 3.6 2.7 - - - +
57B GLU* 2.8 53.4 + - - +
278H LEU* 4.8 7.0 - - - -
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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 72.3 - - - +
51B LEU* 1.3 61.7 + - - +
52B ALA 3.1 33.3 + - - +
53B ASP* 3.9 12.7 + - - +
54B ASP 4.2 1.0 - - - +
55B VAL 3.7 4.0 - - - +
56B TYR* 3.3 37.0 + - + -
277H LEU* 4.4 8.9 + - - +
278H LEU* 3.9 21.1 - - + +
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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* 3.5 40.6 - - + +
30A HIS* 4.2 21.7 - - + +
49B SER* 3.7 9.6 + - - +
50B GLN* 1.3 73.8 - - - +
52B ALA* 1.3 62.2 + - + +
55B VAL* 3.0 18.9 + - + +
56B TYR 4.7 0.2 - - - -
57B GLU* 3.8 18.2 - - + -
83B ILE* 3.8 38.4 - - + -
304E PRO* 5.8 0.4 - - + -
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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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50B GLN* 3.1 19.7 - - - +
51B LEU* 1.3 80.3 - - + +
53B ASP* 1.3 67.3 + - - +
55B VAL* 2.9 34.4 + - + +
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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