Contacts of the helix formed by residues 37 - 49 (chain T) in PDB entry 2KFX
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 SER 37 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35T SER* 4.0 3.3 + - - -
36T ILE* 1.3 80.4 - - - +
38T THR* 1.3 68.8 + - - +
39T LYS* 2.5 35.1 + - - +
40T GLU* 3.0 7.6 + - - +
41T LEU* 2.9 23.4 + - - +
61T ILE* 5.9 5.8 - - - -
70T GLY 4.2 11.9 + - - -
71T THR* 5.8 0.4 - - - -
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Residues in contact with THR 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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37T SER* 1.3 78.0 + - - +
39T LYS* 1.3 67.2 + - - +
41T LEU* 3.8 14.5 + - - +
42T GLY* 4.0 8.0 + - - -
54T PRO* 3.2 51.4 - - - +
57T LEU* 4.8 6.3 - - + +
58T GLN* 3.8 33.7 - - + +
61T ILE* 5.6 5.9 - - + +
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Residues in contact with LYS 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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37T SER* 2.5 21.4 + - - +
38T THR* 1.3 78.0 - - - +
40T GLU* 1.3 77.8 + - + +
41T LEU 3.1 4.4 + - - -
42T GLY* 4.2 4.3 + - - -
43T LYS* 4.3 6.2 + - - +
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Residues in contact with GLU 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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27T PHE* 2.8 45.5 - - - +
28T VAL* 4.9 7.2 - - + -
29T LEU* 5.2 5.0 - - - +
31T ALA* 6.0 2.7 - - + -
35T SER 5.5 2.0 - - - +
36T ILE* 4.9 4.3 - - + -
37T SER* 3.0 10.0 + - - +
39T LYS* 1.3 92.6 - - + +
41T LEU* 1.3 63.1 + - - +
43T LYS* 3.3 39.5 + - + +
44T VAL* 3.8 2.9 + - - +
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Residues in contact with LEU 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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27T PHE* 3.9 11.7 - - + -
36T ILE* 4.0 9.0 - - + -
37T SER 2.9 13.1 + - - +
38T THR* 3.8 11.9 - - - -
39T LYS 3.1 0.8 - - - -
40T GLU* 1.3 74.3 - - - +
42T GLY* 1.3 58.5 + - - +
43T LYS 2.6 15.1 + - - -
44T VAL* 2.9 15.2 + - - +
45T MET* 3.4 31.8 + - + -
57T LEU* 4.2 20.6 - - + -
61T ILE* 4.5 21.3 - - + -
91T WW7 3.8 38.4 - - + +
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Residues in contact with GLY 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 THR 4.0 7.7 + - - -
39T LYS 4.2 2.1 + - - -
41T LEU* 1.3 77.9 - - - +
43T LYS* 1.3 59.9 + - - +
45T MET* 4.0 11.0 - - - +
46T ARG* 3.4 21.3 + - - +
50T GLN 4.8 0.7 - - - +
51T ASN* 4.2 14.7 - - - +
52T PRO* 5.6 5.4 - - - -
57T LEU* 4.2 15.9 - - - +
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Residues in contact with LYS 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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26T ILE* 4.9 11.2 - - + +
29T LEU* 3.6 37.1 - - - +
39T LYS 4.3 5.3 + - - +
40T GLU* 3.3 38.3 + - + +
41T LEU 2.6 5.9 + - - -
42T GLY* 1.3 74.9 - - - +
44T VAL* 1.3 62.8 + - + +
46T ARG* 3.3 19.7 - - - +
47T MET* 4.1 7.6 + - - +
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Residues in contact with VAL 44 (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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26T ILE* 3.8 23.1 - - + -
27T PHE* 3.1 61.5 - - + +
40T GLU 3.8 4.3 - - - +
41T LEU 2.9 1.4 + - - -
43T LYS* 1.3 74.6 - - + +
45T MET* 1.3 60.4 + - + +
46T ARG 2.8 11.4 + - - -
47T MET* 3.0 33.6 + - + +
48T LEU* 3.3 17.1 - - + +
91T WW7 5.6 2.5 - - - +
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Residues in contact with MET 45 (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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27T PHE* 5.3 2.7 - - + -
41T LEU* 3.4 25.5 + - + +
42T GLY* 4.4 8.1 - - - +
43T LYS 3.5 0.2 - - - -
44T VAL* 1.3 77.2 - - + +
46T ARG* 1.3 59.7 + - - +
47T MET 3.4 0.2 - - - -
48T LEU* 3.5 28.7 + - + +
49T GLY 3.4 5.7 + - - -
50T GLN* 2.9 47.9 + - + +
52T PRO* 5.1 4.7 - - + -
57T LEU* 4.9 8.1 - - + -
91T WW7 3.7 44.6 - - + +
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Residues in contact with ARG 46 (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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42T GLY 3.4 12.1 + - - +
43T LYS* 3.3 17.7 - - - +
44T VAL 2.8 0.6 + - - -
45T MET* 1.3 76.4 - - - +
47T MET* 1.3 67.1 + - + +
48T LEU 3.0 2.8 + - - -
49T GLY* 3.7 8.8 + - - -
50T GLN 3.5 11.1 + - - +
51T ASN* 5.2 10.2 + - + +
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Residues in contact with MET 47 (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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26T ILE* 4.1 22.0 - - + -
43T LYS 4.3 7.6 - - - +
44T VAL* 3.0 29.3 + - + +
46T ARG* 1.3 76.7 - - + +
48T LEU* 1.3 71.3 + - + +
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Residues in contact with LEU 48 (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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44T VAL* 3.3 24.7 - - + +
45T MET* 3.6 34.3 - - + +
46T ARG 3.0 2.0 - - - -
47T MET* 1.3 91.6 - - + +
49T GLY* 1.3 59.5 + - - +
50T GLN* 4.7 3.8 - - + +
91T WW7 6.0 1.6 - - - +
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Residues in contact with GLY 49 (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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45T MET 3.4 0.6 + - - -
46T ARG 3.7 5.5 + - - -
48T LEU* 1.3 81.5 - - - +
50T GLN* 1.3 83.0 + - - +
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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