Contacts of the helix formed by residues 31 - 43 (chain T) in PDB entry 5JPQ
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 ASP 31 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29T PRO* 2.8 21.0 + - + +
30T ARG* 1.3 73.7 - - - +
32T LEU* 1.3 65.8 + - - +
33T GLY* 3.3 1.7 + - - +
34T LYS* 3.3 16.9 + - + +
35T ILE* 3.3 23.5 + - - +
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Residues in contact with LEU 32 (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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220S SER 5.5 7.0 - - - +
221S ILE* 6.1 3.8 - - + -
30T ARG 4.3 0.8 - - - -
31T ASP* 1.3 70.4 - - - +
33T GLY* 1.3 64.7 + - - +
35T ILE* 3.6 3.2 + - - +
36T THR* 3.2 26.9 + - - -
119T GLU* 5.5 4.5 - - + +
120T LEU* 5.6 10.1 - - - +
123T GLU* 5.3 13.0 - - + +
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Residues in contact with GLY 33 (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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31T ASP* 3.3 1.8 - - - +
32T LEU* 1.3 81.6 - - - +
34T LYS* 1.3 60.6 + - - +
36T THR* 3.7 4.1 + - - -
37T GLU* 3.3 20.6 + - - +
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Residues in contact with LYS 34 (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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29T PRO* 5.8 5.8 - - + +
31T ASP* 3.3 18.8 + - + +
33T GLY* 1.3 72.6 - - - +
35T ILE* 1.3 65.3 + - - +
37T GLU* 3.5 6.1 + - - +
38T GLU* 3.0 24.3 + - - +
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Residues in contact with ILE 35 (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 VAL* 5.3 16.4 - - + +
28T ASN* 6.1 3.4 - - + -
29T PRO 5.4 5.8 + - - +
31T ASP 3.3 15.0 + - - +
32T LEU* 4.2 3.6 - - - +
34T LYS* 1.3 75.0 - - - +
36T THR* 1.3 66.7 + - - +
38T GLU* 3.0 7.8 + - - +
39T LEU* 2.9 24.9 + - - +
120T LEU* 6.0 6.5 - - + -
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Residues in contact with THR 36 (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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32T LEU 3.2 16.2 + - - -
33T GLY* 3.8 4.3 - - - -
35T ILE* 1.3 77.3 - - - +
37T GLU* 1.3 57.8 + - - +
39T LEU* 3.2 6.6 + - - +
40T LEU* 2.9 29.4 + - - +
120T LEU 5.8 0.9 - - - -
123T GLU* 5.3 8.5 - - - -
124T TYR* 5.0 22.4 - - - -
127T ARG* 5.9 4.9 - - - -
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Residues in contact with GLU 37 (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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33T GLY 3.3 15.5 + - - +
34T LYS* 3.7 6.7 - - - +
35T ILE 3.2 0.2 - - - -
36T THR* 1.3 78.8 - - - +
38T GLU* 1.3 58.6 + - - +
40T LEU* 3.4 7.3 + - - +
41T ASN* 2.8 29.5 + - - +
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Residues in contact with GLU 38 (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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34T LYS 3.0 16.5 + - - +
35T ILE* 3.0 8.5 + - - +
37T GLU* 1.3 73.4 - - - +
39T LEU* 1.3 55.7 + - - +
41T ASN* 3.7 7.4 - - - +
42T ASN* 2.8 32.4 + - - +
46T ILE 4.6 1.6 - - - +
47T PRO 5.9 0.2 - - - -
48T PHE* 5.0 20.1 + - + -
49T SER 5.6 2.0 - - - +
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Residues in contact with LEU 39 (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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35T ILE 2.9 12.4 + - - +
36T THR* 3.5 11.0 - - - +
38T GLU* 1.3 74.3 - - - +
40T LEU* 1.3 63.5 + - - +
42T ASN* 3.3 15.7 + - - +
43T GLU* 3.4 11.1 + - - +
124T TYR* 6.1 4.3 - - + -
142X SER* 6.1 4.9 - - - -
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Residues in contact with LEU 40 (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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36T THR 2.9 14.6 + - - +
37T GLU* 3.6 11.4 - - - +
39T LEU* 1.3 75.0 - - - +
41T ASN* 1.3 61.4 + - - +
43T GLU* 3.4 20.2 - - - +
44T LYS* 4.2 2.6 + - - +
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Residues in contact with ASN 41 (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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37T GLU 2.8 18.5 + - - +
38T GLU* 3.7 8.7 - - - +
40T LEU* 1.3 76.9 - - - +
42T ASN* 1.3 64.8 + - - +
44T LYS* 3.1 16.8 + - - +
45T GLY 3.6 0.2 + - - -
46T ILE* 3.3 31.1 + - + +
47T PRO 6.1 0.2 - - - +
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Residues in contact with ASN 42 (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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38T GLU 2.8 21.3 + - - +
39T LEU* 3.3 11.1 + - - +
41T ASN* 1.3 73.4 - - - +
43T GLU* 1.3 56.7 + - - +
45T GLY* 2.9 19.9 + - - -
46T ILE 3.3 16.6 + - - +
48T PHE 5.9 1.8 - - - +
69T ALA* 5.1 2.3 - - - +
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Residues in contact with GLU 43 (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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39T LEU 3.4 7.9 + - - +
40T LEU* 3.4 16.2 - - - +
41T ASN 3.1 0.2 - - - -
42T ASN* 1.3 78.1 - - - +
44T LYS* 1.3 57.7 + - - +
45T GLY 3.2 0.8 + - - -
69T ALA* 4.6 8.3 - - - +
139X SER* 6.3 3.4 - - - -
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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