Contacts of the helix formed by residues 15 - 26 (chain D) in PDB entry 4K81
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 GLY 15 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13D GLY* 3.2 5.6 - - - -
14D VAL* 1.3 78.9 - - - +
16D LYS* 1.3 68.1 - - - +
17D SER 3.3 3.4 - - - -
18D ALA* 3.3 12.8 + - - +
19D LEU* 2.9 31.9 + - - +
81D VAL* 4.9 0.2 - - - -
116D ASN* 3.6 11.4 - - - -
117D LYS* 4.9 2.7 - - - -
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Residues in contact with LYS 16 (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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8D VAL* 3.7 22.0 - - + +
9D VAL* 3.3 35.9 - - - +
10D GLY* 3.3 12.7 + - - +
11D ALA 3.0 23.8 + - - -
12D VAL* 4.5 0.4 - - - +
13D GLY 4.5 5.9 - - - +
14D VAL* 3.7 13.9 - - + +
15D GLY* 1.3 76.3 - - - +
17D SER* 1.3 62.3 + - - +
19D LEU* 3.4 5.5 + - - +
20D THR* 2.8 28.9 + - - -
57D ASP* 3.5 12.1 - - - +
58D THR* 3.3 28.0 - - - -
60D GLY* 3.8 12.5 - - - +
81D VAL* 4.3 2.9 - - + +
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Residues in contact with SER 17 (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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15D GLY 3.3 0.4 - - - -
16D LYS* 1.3 77.9 - - - +
18D ALA* 1.3 62.6 + - - +
20D THR* 3.3 1.4 + - - -
21D ILE* 3.0 42.7 + - - +
33D ASP 5.2 5.2 - - - -
35D THR* 2.7 22.9 + - - -
40D TYR* 5.6 0.2 - - - -
57D ASP* 2.5 30.3 + - - -
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Residues in contact with ALA 18 (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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15D GLY* 3.3 14.3 + - - +
17D SER* 1.3 79.5 - - - +
19D LEU* 1.3 60.7 + - - +
21D ILE* 4.0 5.8 - - - +
22D GLN* 3.0 26.5 + - - +
27D HIS 4.8 1.4 - - - +
28D PHE* 4.5 8.4 - - + -
29D VAL* 4.5 23.9 + - + +
146D ALA* 3.5 23.5 - - + +
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Residues in contact with LEU 19 (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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8D VAL* 5.7 1.8 - - + -
15D GLY 2.9 19.9 + - - +
16D LYS* 3.9 3.4 - - - +
18D ALA* 1.3 77.0 - - - +
20D THR* 1.3 65.3 + - - +
22D GLN* 3.6 3.4 - - - +
23D LEU* 3.0 23.6 + - - +
79D LEU* 5.6 3.8 - - + -
81D VAL* 4.0 17.7 - - + -
114D VAL* 3.8 18.6 - - + -
116D ASN* 3.7 18.4 - - - +
144D THR* 3.6 29.8 - - + +
146D ALA* 3.8 10.1 - - + +
152D VAL* 3.7 32.2 - - + +
155D ALA* 6.4 0.7 - - + -
156D PHE* 4.3 12.6 - - + -
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Residues in contact with THR 20 (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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8D VAL* 3.7 20.6 - - - +
16D LYS 2.8 17.2 + - - -
17D SER* 3.8 6.5 - - - -
19D LEU* 1.3 76.6 - - - +
21D ILE* 1.3 58.1 + - - +
23D LEU* 3.3 3.0 + - - +
24D ILE* 2.9 36.1 + - + +
40D TYR* 3.6 37.0 - - + -
55D ILE* 3.7 22.7 - - + -
57D ASP* 4.5 6.7 - - + +
156D PHE* 3.9 11.3 - - + -
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Residues in contact with ILE 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C ARG* 5.8 4.9 - - - +
17D SER* 3.0 32.8 + - - +
18D ALA* 4.0 3.1 - - - +
20D THR* 1.3 74.1 - - - +
22D GLN* 1.3 60.4 + - - +
24D ILE* 4.3 4.0 - - - +
25D GLN* 2.6 44.8 + - - +
26D ASN 3.4 0.9 + - - -
27D HIS* 3.7 34.3 - - - +
29D VAL* 3.9 28.3 - - + -
40D TYR* 3.9 31.2 - - + +
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Residues in contact with GLN 22 (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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191A TYR* 3.9 11.9 - - - -
18D ALA 3.0 19.4 + - - +
19D LEU* 3.6 5.8 - - - +
21D ILE* 1.3 76.9 - - - +
23D LEU* 1.3 57.7 + - - +
26D ASN* 3.1 12.1 + - - -
27D HIS 2.9 41.7 + - - +
28D PHE* 4.1 5.1 - - - +
146D ALA 3.3 24.0 + - - +
147D LYS 4.2 6.3 + - - -
149D ARG* 2.2 79.1 + - + +
152D VAL* 4.3 12.1 - - + -
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Residues in contact with LEU 23 (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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115A GLU* 4.8 0.2 - - - +
19D LEU 3.0 14.9 + - - +
20D THR 3.4 7.4 - - - +
22D GLN* 1.3 79.0 - - - +
24D ILE* 1.3 64.0 + - + +
26D ASN* 5.0 0.3 + - - +
42D LYS* 2.7 41.4 + - + +
53D LEU* 4.5 8.5 - - + -
55D ILE* 3.6 31.0 - - + -
149D ARG* 4.2 4.4 + - - +
152D VAL* 4.0 8.8 - - + +
153D GLU* 4.1 30.3 - - + -
156D PHE* 3.7 33.9 - - + -
157D TYR* 4.3 12.8 - - + -
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Residues in contact with ILE 24 (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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115A GLU* 5.4 2.6 - - - +
20D THR* 2.9 22.0 + - + +
21D ILE* 4.1 1.8 - - - +
23D LEU* 1.3 91.7 - - + +
25D GLN* 1.3 75.0 + - + +
26D ASN* 3.6 1.5 + - - +
40D TYR* 3.7 36.1 - - + -
41D ARG 3.8 18.6 - - - +
42D LYS* 3.5 37.2 + - + +
55D ILE* 4.3 4.7 - - + -
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Residues in contact with GLN 25 (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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189A LYS* 4.2 6.2 + - - -
21D ILE* 2.6 27.9 + - - +
24D ILE* 1.3 86.9 - - + +
26D ASN* 1.3 68.3 + - - +
27D HIS* 2.8 36.3 + - + +
40D TYR* 4.4 19.4 - - - -
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Residues in contact with ASN 26 (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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115A GLU* 4.5 13.3 + - - +
188A ARG* 4.0 16.9 - - - +
189A LYS* 3.3 49.1 + - - +
191A TYR* 2.3 28.3 + - - -
21D ILE 3.4 0.6 + - - -
22D GLN* 3.1 23.7 + - - +
23D LEU 4.7 0.4 - - - +
24D ILE 3.6 1.4 - - - +
25D GLN* 1.3 79.3 - - - +
27D HIS* 1.3 50.9 + - - +
149D ARG* 3.4 33.1 + - - +
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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