Contacts of the helix formed by residues 38 - 50 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A ASN* 3.8 19.1 - - - -
10A THR* 3.5 13.0 + - - +
12A ASP* 4.4 3.2 + - - -
37A GLY* 1.3 72.5 - - - -
39A LYS* 1.3 61.3 + - - -
40A GLY 3.2 2.9 - - - -
41A ALA 3.3 2.0 + - - -
42A ASN* 2.9 36.6 + - - +
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Residues in contact with LYS 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ASN* 3.5 4.9 + - - +
38A GLY* 1.3 71.4 - - - -
40A GLY* 1.3 63.2 + - - +
42A ASN* 4.5 0.2 - - - +
43A GLN* 3.0 30.5 + - - +
136A GLN* 3.8 15.3 - - + -
138A ASN* 4.4 6.0 - - - +
161A ASN* 3.4 28.2 - - - +
163A SER* 3.3 38.8 + - - +
164A PRO* 4.6 4.9 - - + -
231A GLY 5.1 0.4 - - - -
232A ASP* 2.8 38.4 + - - +
900A ATP 3.9 30.7 + - - -
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Residues in contact with GLY 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A VAL* 3.7 8.5 - - - +
7A GLY* 4.5 1.1 - - - -
8A ASN* 3.1 22.9 - - - +
39A LYS* 1.3 78.2 - - - +
41A ALA* 1.3 55.9 + - - +
43A GLN* 3.9 0.5 - - - -
44A ALA* 3.0 30.3 + - - +
56A LEU* 3.8 6.7 - - - -
136A GLN* 3.3 24.9 + - - -
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Residues in contact with ALA 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ASN 3.0 9.4 + - - +
9A ILE* 3.5 38.6 - - + -
36A ILE* 4.4 7.4 - - + -
37A GLY 3.6 14.1 - - - +
38A GLY 3.3 1.0 + - - -
40A GLY* 1.3 72.6 - - - +
42A ASN* 1.3 61.3 + - - +
45A ILE* 2.8 39.9 + - + +
56A LEU* 3.7 15.0 - - + -
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Residues in contact with ASN 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ASP* 5.8 0.2 + - - -
36A ILE 4.0 6.1 - - - +
37A GLY* 3.9 14.8 - - - -
38A GLY 2.9 28.4 + - - +
39A LYS 4.0 0.2 - - - +
41A ALA* 1.3 75.1 - - - +
43A GLN* 1.3 62.3 + - - +
45A ILE* 3.9 3.0 - - - +
46A ILE* 3.1 32.6 + - - +
228A THR* 5.5 1.8 - - - +
229A GLY* 4.4 5.5 - - - +
232A ASP* 3.0 34.4 + - + +
270A THR* 4.3 7.7 - - - +
271A LEU* 4.6 3.1 - - - +
274A PHE* 3.7 33.4 - - + -
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Residues in contact with GLN 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A LYS* 3.0 16.9 + - - +
40A GLY 3.9 1.8 - - - +
42A ASN* 1.3 76.8 - - - +
44A ALA* 1.3 62.6 + - - +
47A LEU* 3.0 30.1 + - - +
134A LEU* 3.5 23.4 - - + +
136A GLN* 2.8 27.5 + - - +
161A ASN* 3.1 26.3 - - - +
231A GLY 5.0 0.2 + - - -
232A ASP* 3.0 44.1 + - + +
235A LEU* 3.7 18.1 - - + +
236A ALA* 3.6 11.0 - - + +
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Residues in contact with ALA 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A VAL* 3.8 21.0 - - + +
40A GLY 3.0 18.1 + - - +
41A ALA 3.8 1.8 - - - +
43A GLN* 1.3 77.1 - - - +
45A ILE* 1.3 58.3 + - - +
47A LEU* 3.4 4.4 + - - +
48A SER* 3.0 27.7 + - - -
54A THR* 3.7 15.2 - - + +
56A LEU* 3.9 15.3 - - + -
78A LEU* 3.7 19.2 - - + +
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Residues in contact with ILE 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ILE* 4.5 2.9 - - + -
41A ALA* 2.8 35.6 + - + +
42A ASN* 3.9 3.8 - - - +
44A ALA* 1.3 73.9 - - - +
46A ILE* 1.3 60.3 + - + +
48A SER* 2.6 22.8 + - - -
49A ARG* 3.0 24.2 + - - +
73A ILE* 3.7 23.8 - - + -
76A GLU* 3.5 34.1 - - + +
78A LEU* 3.7 17.3 - - + -
271A LEU* 3.8 33.7 - - + -
274A PHE* 5.1 1.8 - - + -
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Residues in contact with ILE 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ASN 3.1 17.9 + - - +
45A ILE* 1.3 77.5 - - + +
47A LEU* 1.3 63.1 + - - +
49A ARG* 3.1 18.2 + - - +
50A CYS* 3.1 16.3 + - - -
232A ASP* 4.4 2.2 - - + -
233A THR* 3.3 41.1 - - + +
236A ALA* 3.5 20.0 - - + -
237A VAL* 4.0 20.6 - - + -
274A PHE* 3.6 42.4 - - + -
275A PRO* 5.0 2.0 - - + -
280A LEU* 4.6 7.9 - - + -
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Residues in contact with LEU 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A VAL* 3.9 20.2 - - + -
5A VAL* 4.4 0.4 - - + -
43A GLN 3.0 21.9 + - - +
44A ALA* 3.5 8.7 - - - +
46A ILE* 1.3 78.2 - - - +
48A SER* 1.3 61.6 + - - +
50A CYS* 3.1 15.3 + - - +
52A ILE* 3.2 31.9 + - + +
54A THR* 3.6 10.8 - - + +
134A LEU* 3.8 27.6 - - + -
236A ALA* 3.4 29.2 - - + +
239A LEU* 4.2 15.7 - - + -
240A ALA* 4.0 16.8 - - + +
243A LEU* 4.8 1.6 - - + -
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Residues in contact with SER 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ALA 3.0 13.1 + - - -
45A ILE* 2.6 25.1 + - - +
47A LEU* 1.3 75.9 - - - +
49A ARG* 1.3 57.2 + - - +
51A GLY* 3.0 18.9 + - - -
52A ILE 3.4 15.2 - - - +
54A THR* 3.7 4.2 + - - -
76A GLU* 4.8 0.2 - - - +
77A PRO* 3.5 46.5 - - - +
78A LEU* 3.8 13.8 - - - +
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Residues in contact with ARG 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ILE* 3.0 24.2 + - - +
46A ILE* 3.1 14.8 + - - +
48A SER* 1.3 78.5 + - - +
50A CYS* 1.3 58.5 + - - +
51A GLY* 3.1 1.6 + - - -
76A GLU* 2.8 42.0 + - - +
77A PRO* 4.3 6.3 - - + -
271A LEU* 3.1 29.4 + - - +
274A PHE* 3.4 23.4 + - - +
275A PRO 2.9 28.3 + - - -
276A GLY* 3.9 5.2 - - - -
277A SER* 3.0 47.1 + - - +
280A LEU* 3.5 12.8 - - + +
125B ALA* 3.8 20.0 + - - +
154B ARG* 5.5 0.2 - - - +
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Residues in contact with CYS 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ILE 3.1 18.8 + - - -
47A LEU* 3.1 10.2 + - - +
49A ARG* 1.3 76.1 - - - +
51A GLY* 1.3 59.9 + - - +
52A ILE* 3.5 0.8 + - + -
237A VAL* 4.2 14.1 - - - -
240A ALA* 3.5 30.7 - - + -
244A LEU* 3.8 19.6 - - - +
280A LEU* 3.7 28.9 - - - -
281A ALA 6.1 0.2 - - - +
284A LEU* 4.1 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