Contacts of the strand formed by residues 39 - 52 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37D GLN 3.8 2.2 + - - -
38D PRO* 1.3 70.3 - - - +
40D VAL* 1.3 64.6 + - - +
65D THR 4.1 0.5 - - - +
66D ALA* 3.8 0.2 - - - -
67D SER* 3.0 52.5 + - - +
68D LEU* 4.4 1.5 - - - +
293G PRO* 3.4 22.3 - - + +
294G LYS* 3.5 33.9 + - - +
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Residues in contact with VAL 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D PRO* 4.5 7.2 - - + +
39D GLU* 1.3 79.3 - - - +
41D LYS* 1.3 60.6 + - - +
64D VAL* 5.0 2.5 - - + -
65D THR 3.7 3.4 - - - +
66D ALA* 4.3 19.5 - - + -
74D PHE* 5.2 2.0 - - + -
126D LEU* 3.8 23.1 - - + -
307E THR* 6.0 0.7 - - + -
290G TRP* 3.2 49.1 - - + +
292G GLY 4.2 4.5 - - - +
293G PRO* 3.0 22.9 + - - +
294G LYS* 5.2 0.4 - - - -
295G ALA 5.4 1.6 - - - +
296G THR* 4.3 18.6 - - + +
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Residues in contact with LYS 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D VAL* 1.3 73.2 - - - +
42D LEU* 1.3 80.1 + - - +
43D ASP* 2.9 35.6 + - - +
63D THR 3.8 0.3 - - - +
64D VAL* 3.6 5.5 - - - +
65D THR* 2.9 48.3 + - + +
285G ASN* 4.7 3.8 - - - +
288G VAL 5.2 5.2 - - - +
290G TRP* 3.3 11.4 + - + +
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Residues in contact with LEU 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D LYS* 1.3 88.5 - - - +
43D ASP* 1.3 75.5 + - - +
44D LEU* 3.8 23.6 - - + +
62D VAL* 3.8 18.8 - - + -
63D THR 3.4 8.1 - - - +
64D VAL* 5.1 2.0 - - + -
107D PHE* 5.3 8.5 - - + -
128D LEU* 3.6 27.4 - - + -
286G MET 5.4 1.7 - - - +
288G VAL* 3.8 37.1 + - + +
290G TRP* 3.3 30.5 - - + +
291G LEU* 6.2 1.3 - - + -
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Residues in contact with ASP 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D LYS* 2.9 40.4 + - - +
42D LEU* 1.3 76.5 - - - +
44D LEU* 1.3 62.9 + - - +
62D VAL 3.9 0.2 - - - -
63D THR* 2.9 49.8 + - + +
65D THR* 4.4 10.2 + - - -
285G ASN* 2.9 25.6 + - - +
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Residues in contact with LEU 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D LEU* 3.8 25.8 - - + +
43D ASP* 1.3 80.5 - - - +
45D ASP* 1.3 63.3 + - - +
60D LEU* 5.0 12.6 - - + -
61D ARG 3.6 7.6 - - - +
62D VAL* 5.5 2.0 - - + -
63D THR* 5.8 0.4 - - - -
107D PHE* 5.3 7.4 - - + -
133D PHE* 4.2 14.8 - - + -
284G GLY* 3.7 1.2 - - - -
285G ASN* 2.9 32.2 + - - +
286G MET* 3.5 54.1 - - + +
288G VAL* 3.8 28.0 - - + -
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Residues in contact with ASP 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D LEU* 1.3 77.1 - - - +
46D THR* 1.3 82.7 + - - +
60D LEU* 3.8 7.9 - - - +
61D ARG* 2.8 77.9 + - - +
281G PHE* 5.7 1.1 - - - -
282G ALA 4.1 11.4 - - - +
283G ASP 4.2 8.8 - - - +
284G GLY* 4.5 6.2 - - - -
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Residues in contact with THR 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D ASP* 1.3 92.7 + - - +
47D ALA* 1.3 74.0 + - - +
48D SER* 5.6 0.5 - - - -
58D VAL* 4.5 5.7 - - - +
59D VAL* 2.9 17.2 + - - -
60D LEU* 4.3 2.5 - - - +
61D ARG* 4.6 1.3 - - - +
281G PHE* 3.3 60.9 + - + +
282G ALA* 3.7 19.8 + - - +
284G GLY 5.5 1.6 - - - +
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Residues in contact with ALA 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D ASP* 5.5 0.2 - - - +
46D THR* 1.3 83.0 + - - +
48D SER* 1.3 63.4 + - - +
58D VAL* 3.9 2.9 - - - +
59D VAL* 2.9 52.1 + - + +
61D ARG* 5.8 4.3 - - - +
79D GLN* 5.5 3.8 - - - +
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Residues in contact with SER 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D THR* 5.6 0.9 - - - -
47D ALA* 1.3 77.9 - - - +
49D SER* 1.3 66.7 + - - +
57D GLU* 3.6 7.0 - - - -
58D VAL* 6.4 0.2 - - - -
59D VAL* 5.0 1.3 - - - +
278G LEU* 3.6 35.9 + - - -
279G GLY* 5.1 4.7 - - - -
281G PHE 5.6 2.6 + - - -
282G ALA* 5.9 2.9 - - - +
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Residues in contact with SER 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C PRO* 5.7 0.2 - - - +
19D LYS* 5.3 0.5 + - - -
48D SER* 1.3 77.3 - - - +
50D GLN* 1.3 66.4 + - - +
51D LEU* 3.5 9.4 + - - +
57D GLU* 3.2 44.5 + - - +
278G LEU* 3.4 9.4 - - - +
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Residues in contact with GLN 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D SER* 1.3 73.0 - - - +
51D LEU* 1.3 60.6 - - - +
52D ALA* 3.0 32.3 + - - +
53D ASP* 4.5 2.2 - - - +
54D ASP 4.3 3.8 - - - +
55D VAL 3.5 7.9 - - - +
56D TYR* 3.5 30.1 + - + -
274G GLN* 2.9 41.6 + - - -
278G LEU* 3.7 4.0 - - + +
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Residues in contact with LEU 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C PRO* 3.8 32.8 - - + -
49D SER* 3.7 23.3 - - - +
50D GLN* 1.3 75.8 - - - +
52D ALA* 1.3 64.1 + - + +
55D VAL* 3.0 16.2 + - + -
57D GLU* 3.7 24.5 - - + +
83D ILE* 3.6 46.0 - - + -
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Residues in contact with ALA 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D GLN* 3.0 25.4 + - - +
51D LEU* 1.3 79.2 - - + +
53D ASP* 1.3 67.9 + - + +
55D VAL* 3.0 31.2 + - + +
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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