Contacts of the helix formed by residues 42 - 52 (chain N) in PDB entry 1K2V
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 42 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1N DEF 4.3 10.2 - - - +
40N ALA* 3.3 1.2 - - - +
41N LEU* 1.3 77.9 - - - +
43N TRP* 1.3 85.1 + - - +
44N LEU* 3.0 19.3 + - - +
45N PRO* 3.2 15.5 - - + +
46N VAL* 3.2 13.5 - - - +
84N ARG* 2.9 32.9 + - - +
101N VAL 4.1 2.0 + - - -
102N TRP* 4.3 1.1 - - + -
103N SER* 2.5 46.7 + - - +
106N TYR* 3.4 34.1 - - + -
217N TRP* 5.4 1.4 - - - -
273N TRP* 4.4 4.6 + - - -
275N TYR 5.0 1.0 - - - +
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Residues in contact with TRP 43 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1N DEF 3.7 14.6 - - + -
42N GLU* 1.3 82.3 + - - +
44N LEU* 1.3 67.2 + - - +
46N VAL* 3.3 12.2 + - + +
47N GLU* 3.1 20.3 + - - +
59N VAL* 4.6 0.9 - - + -
60N ALA 3.0 25.5 + - - -
61N ASP* 3.4 10.4 + - - -
64N ASN* 3.5 31.0 - - + -
65N TYR* 3.3 39.8 - + + +
68N TRP* 3.9 8.1 - - + -
69N VAL* 3.7 19.0 - - + +
84N ARG* 3.5 31.7 - - - +
273N TRP* 3.5 53.8 - + + +
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Residues in contact with LEU 44 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42N GLU* 3.0 15.0 + - - +
43N TRP* 1.3 75.0 - - - +
45N PRO* 1.3 69.8 - - + +
47N GLU* 3.0 18.1 + - - +
48N LEU* 3.0 21.5 + - + +
103N SER* 4.0 10.5 - - - +
122N PHE* 4.1 10.3 - - + +
123N ASN 3.8 11.2 - - - +
124N PHE* 3.6 37.2 - - + +
134N ALA* 5.8 2.5 - - + -
137N SER* 5.7 2.0 - - - -
217N TRP* 5.6 0.9 - - + -
273N TRP* 4.6 1.6 - - - +
275N TYR 3.9 11.7 - - - +
276N GLY* 3.6 32.8 - - - +
277N ALA* 3.8 13.2 - - + -
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Residues in contact with PRO 45 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40N ALA* 4.5 1.6 - - + -
42N GLU 3.2 16.4 - - - +
44N LEU* 1.3 95.7 - - + +
46N VAL* 1.3 63.1 + - - +
47N GLU 3.2 0.2 - - - -
48N LEU* 3.6 11.9 - - + +
49N LEU* 2.9 30.2 + - - +
101N VAL* 3.6 28.7 - - + +
102N TRP* 3.8 29.8 - - - +
103N SER* 3.4 12.8 - - - +
122N PHE* 4.4 4.9 - - + -
141N MET* 4.1 6.2 - - + +
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Residues in contact with VAL 46 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40N ALA* 3.5 20.8 - - + +
42N GLU 3.2 17.9 + - - +
43N TRP* 3.4 15.5 - - + +
44N LEU 3.1 0.4 - - - -
45N PRO* 1.3 76.6 - - - +
47N GLU* 1.3 60.3 + - - +
49N LEU* 3.1 6.7 + - - +
50N LEU* 2.9 50.4 + - + +
56N PRO* 4.6 2.5 - - + -
59N VAL* 3.8 24.9 - - + -
65N TYR* 3.7 21.8 - - + -
74N LEU* 3.8 14.4 - - + -
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Residues in contact with GLU 47 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43N TRP 3.1 7.2 + - - +
44N LEU 3.0 10.0 + - - +
46N VAL* 1.3 82.0 - - - +
48N LEU* 1.3 60.1 + - - +
50N LEU* 4.5 7.0 - - - -
51N ALA* 3.0 24.7 + - + +
65N TYR* 5.4 3.8 - - + +
69N VAL* 5.4 5.6 - - + +
72N PRO* 5.3 3.4 - - + -
273N TRP* 4.8 1.6 - - - -
276N GLY* 3.2 5.9 - - - -
277N ALA* 2.8 31.4 + - + +
278N THR* 5.5 0.2 - - - +
279N LEU* 2.5 48.5 + - + +
280N SER* 2.7 33.0 + - - -
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Residues in contact with LEU 48 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44N LEU* 3.0 17.3 + - + +
45N PRO* 3.6 15.5 - - + +
46N VAL 3.2 0.2 - - - -
47N GLU* 1.3 77.8 - - - +
49N LEU* 1.3 64.8 + - - +
51N ALA* 3.5 0.4 + - - -
52N LEU* 3.4 26.6 + - - +
122N PHE* 3.7 39.5 - - + -
134N ALA 4.3 2.5 - - - +
137N SER* 3.7 15.9 - - - +
138N LEU* 3.7 34.0 - - + +
141N MET* 3.9 17.3 - - + -
277N ALA* 3.9 25.6 - - + -
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Residues in contact with LEU 49 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38N ILE* 3.7 30.3 - - + -
40N ALA* 4.1 8.3 - - + -
45N PRO 2.9 21.4 + - - +
46N VAL 3.5 4.0 - - - +
48N LEU* 1.3 77.0 - - - +
50N LEU* 1.3 59.9 + - - +
52N LEU* 3.0 11.4 + - - +
54N ILE* 2.9 44.8 + - + +
56N PRO* 4.0 22.9 - - + -
101N VAL* 4.0 9.9 - - + -
141N MET* 3.6 31.4 - - + -
145N LEU* 4.0 17.9 - - + -
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Residues in contact with LEU 50 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46N VAL* 2.9 30.5 + - + +
47N GLU* 3.9 4.7 - - - +
49N LEU* 1.3 73.9 - - - +
51N ALA* 1.3 65.0 + - - +
53N GLY* 3.0 13.9 + - - -
54N ILE 3.4 19.3 - - - +
55N VAL* 4.9 2.7 - - + -
56N PRO* 3.8 15.3 - - + -
65N TYR* 3.6 24.2 - - - +
72N PRO* 3.8 17.0 - - + +
73N PRO 4.4 7.9 - - - +
74N LEU* 3.9 11.9 - - + -
75N PRO* 5.4 4.5 - - + -
279N LEU* 4.2 9.9 - - + -
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Residues in contact with ALA 51 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47N GLU 3.0 18.9 + - - +
49N LEU 3.3 0.2 - - - -
50N LEU* 1.3 76.7 - - - +
52N LEU* 1.3 60.3 + - - +
53N GLY 3.3 1.0 + - - -
138N LEU* 3.8 22.0 - - + -
150N ALA* 4.8 2.1 - - - +
154N HIS* 3.7 46.9 - - + +
278N THR* 4.8 1.3 - - - +
279N LEU* 4.0 14.1 - - + +
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Residues in contact with LEU 52 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48N LEU 3.4 10.7 + - - +
49N LEU* 3.0 9.5 + - - +
50N LEU 3.0 0.6 - - - -
51N ALA* 1.3 80.6 - - - +
53N GLY* 1.3 60.0 + - - +
54N ILE* 3.3 2.8 + - + +
138N LEU* 3.7 16.4 - - + +
141N MET* 3.5 33.7 - - + +
142N ALA* 3.6 22.2 - - + +
145N LEU* 4.9 2.0 - - + -
147N LEU* 3.8 31.6 - - + +
150N ALA* 4.1 14.4 - - + +
151N ALA* 3.5 41.1 - - + +
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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