Contacts of the helix formed by residues 38 - 50 (chain B) in PDB entry 3IKH
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 38 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8B ASN* 3.6 14.6 - - - -
10B THR* 3.4 18.7 + - - -
12B ASP* 4.5 3.2 + - - -
37B GLY* 1.3 70.1 - - - -
39B LYS* 1.3 57.4 + - - -
40B GLY 3.2 2.2 - - - -
41B ALA 3.2 2.9 + - - -
42B ASN* 2.7 42.9 + - - +
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Residues in contact with LYS 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B ASN* 3.3 5.0 + - - +
38B GLY* 1.3 71.6 - - - -
40B GLY* 1.3 62.3 + - - +
42B ASN* 4.3 0.4 - - - +
43B GLN* 3.0 31.2 + - - +
136B GLN* 3.9 9.6 - - + -
138B ASN* 3.7 16.6 - - - +
161B ASN* 3.3 28.2 - - - +
163B SER* 3.2 40.5 + - - +
164B PRO* 4.3 4.7 - - + -
231B GLY 5.2 0.6 - - - -
232B ASP* 2.8 36.8 + - - +
900B ATP 3.2 26.5 + - - -
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Residues in contact with GLY 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B VAL* 3.8 6.7 - - - +
7B GLY* 4.3 4.5 - - - -
8B ASN* 3.3 21.0 + - - -
38B GLY 3.2 0.8 - - - -
39B LYS* 1.3 79.7 - - - +
41B ALA* 1.3 56.0 - - - +
43B GLN 3.8 0.2 - - - -
44B ALA* 2.9 31.0 + - - +
56B LEU* 4.0 6.5 - - - -
136B GLN* 3.3 22.6 + - - -
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Residues in contact with ALA 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B ASN 3.0 8.8 + - - +
9B ILE* 3.5 29.2 - - + -
36B ILE* 4.1 9.0 - - + -
37B GLY 3.4 22.2 - - - +
38B GLY 3.2 0.8 + - - -
40B GLY* 1.3 71.1 - - - +
42B ASN* 1.3 61.3 + - - +
45B ILE* 2.8 40.3 + - + +
56B LEU* 3.6 14.3 - - + +
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Residues in contact with ASN 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B ILE* 4.0 3.6 - - - +
37B GLY* 3.5 17.0 - - - -
38B GLY 2.7 33.9 + - - +
39B LYS 3.8 1.3 - - - +
41B ALA* 1.3 73.6 - - - +
43B GLN* 1.3 62.0 + - - +
45B ILE* 4.1 3.5 - - - +
46B ILE* 3.2 29.9 + - - +
228B THR* 5.7 0.8 - - - +
229B GLY* 4.5 3.0 - - - -
232B ASP* 3.0 34.4 + - + +
270B THR* 3.5 21.0 - - - +
271B LEU* 5.3 0.7 - - - +
274B PHE* 3.6 25.3 - - + -
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Residues in contact with GLN 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LYS 3.0 12.9 + - - +
40B GLY 4.0 1.8 - - - +
42B ASN* 1.3 75.5 - - - +
44B ALA* 1.3 63.1 + - - +
47B LEU* 3.0 29.2 + - - +
134B LEU* 3.4 24.5 - - + +
136B GLN* 2.9 30.6 + - - +
161B ASN* 3.1 27.1 - - - +
231B GLY 5.1 0.2 + - - -
232B ASP* 2.9 42.3 + - + +
235B LEU* 3.6 17.8 - - + +
236B ALA* 3.6 12.0 - - + +
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Residues in contact with ALA 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B VAL* 3.9 22.5 - - + +
40B GLY 2.9 18.4 + - - +
41B ALA 3.9 2.2 - - - +
43B GLN* 1.3 77.6 - - - +
45B ILE* 1.3 62.6 + - - +
47B LEU* 3.3 4.1 + - - +
48B SER* 3.0 24.1 + - - -
54B THR* 3.8 5.3 - - - +
56B LEU* 3.9 17.5 - - + -
78B LEU* 3.6 23.1 - - + +
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Residues in contact with ILE 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B ILE* 4.0 27.6 - - + -
41B ALA* 2.8 29.7 + - + +
42B ASN* 4.1 3.8 - - - +
44B ALA* 1.3 71.4 - - - +
46B ILE* 1.3 60.1 + - + +
48B SER* 2.6 22.8 + - - -
49B ARG* 2.9 20.3 + - - +
73B ILE* 4.4 14.1 - - + -
76B GLU* 3.7 30.3 - - + +
78B LEU* 3.4 20.0 - - + -
271B LEU* 3.7 35.0 - - + -
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Residues in contact with ILE 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B ASN 3.2 17.9 + - - +
45B ILE* 1.3 76.5 - - + +
47B LEU* 1.3 63.2 + - - +
49B ARG* 3.1 11.5 + - - +
50B CYS* 3.1 22.1 + - - -
232B ASP 4.3 2.0 - - - +
233B THR* 3.4 42.8 - - + +
236B ALA* 3.4 21.1 - - + -
237B VAL* 3.8 23.8 - - + +
274B PHE* 3.7 35.2 - - + -
275B PRO* 5.4 2.0 - - + +
280B LEU* 4.5 10.8 - - + -
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Residues in contact with LEU 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B VAL* 3.9 24.2 - - + -
5B VAL* 4.2 6.1 - - + -
43B GLN 3.0 23.8 + - - +
44B ALA* 3.5 4.9 - - - +
46B ILE* 1.3 77.2 - - - +
48B SER* 1.3 62.8 + - - +
50B CYS* 3.1 17.0 + - - +
52B ILE* 3.3 32.7 + - + +
54B THR* 3.7 10.8 - - + +
134B LEU* 3.9 22.0 - - + -
236B ALA* 3.5 28.7 - - + +
239B LEU* 4.2 15.5 - - + -
240B ALA* 4.1 15.5 - - + +
243B LEU* 4.7 1.8 - - + -
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Residues in contact with SER 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ALA 3.0 12.5 + - - -
45B ILE* 2.6 26.2 + - - +
47B LEU* 1.3 78.2 - - - +
49B ARG* 1.3 57.0 + - - +
51B GLY* 3.0 19.6 + - - -
52B ILE 3.6 11.9 + - - +
54B THR* 3.7 4.9 + - - -
77B PRO* 3.4 43.8 - - - +
78B LEU* 3.7 19.5 - - - +
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Residues in contact with ARG 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ILE* 2.9 22.6 + - - +
46B ILE* 3.1 12.5 + - - +
48B SER* 1.3 77.7 + - - +
50B CYS* 1.3 59.0 + - - +
51B GLY 3.1 1.2 + - - -
76B GLU* 2.9 43.2 + - - +
77B PRO* 4.4 4.9 - - + -
271B LEU* 3.6 25.7 + - - +
274B PHE* 3.6 22.0 + - - +
275B PRO 3.0 27.4 + - - -
276B GLY* 3.9 10.9 - - - -
277B SER* 3.4 41.0 + - - +
280B LEU* 3.6 14.0 - - + +
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Residues in contact with CYS 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B ILE* 3.1 16.8 + - - -
47B LEU 3.1 11.9 + - - +
49B ARG* 1.3 76.2 - - - +
51B GLY* 1.3 58.7 + - - +
52B ILE* 4.4 1.3 - - + -
237B VAL* 4.3 15.3 - - - -
240B ALA* 3.6 31.4 - - + -
244B LEU* 3.7 20.3 - - - +
280B LEU* 3.5 26.7 - - - -
281B ALA 5.9 0.4 - - - +
284B LEU* 3.8 17.7 - - + +
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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