Contacts of the helix formed by residues 38 - 50 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8D ASN* 3.7 17.0 - - - -
10D THR* 3.8 6.7 - - - -
37D GLY* 1.3 74.1 - - - -
39D LYS* 1.3 68.2 + - - -
40D GLY 3.2 2.9 - - - -
41D ALA 3.3 1.2 + - - -
42D ASN* 2.9 28.5 + - - -
501D GOL 3.1 24.8 + - - -
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Residues in contact with LYS 39 (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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26B SER* 5.2 9.0 + - - -
8D ASN* 3.1 4.8 + - - +
38D GLY* 1.3 70.7 - - - +
40D GLY* 1.3 63.2 + - - +
42D ASN* 3.8 0.9 + - - +
43D GLN* 3.3 29.3 + - - +
105D ILE* 5.8 2.3 - - - +
136D GLN* 3.5 18.8 - - + -
138D ASN* 3.6 21.3 - - - +
161D ASN* 4.5 6.3 - - - +
163D SER* 3.2 41.1 + - - +
164D PRO* 4.6 4.9 - - + -
232D ASP* 3.5 22.1 + - - +
501D GOL 4.0 24.6 + - - +
900D ATP 3.4 32.9 + - - -
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Residues in contact with GLY 40 (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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5D VAL* 3.7 11.1 - - - +
7D GLY* 4.3 1.3 - - - -
8D ASN* 3.4 18.4 + - - -
38D GLY 3.2 0.4 - - - -
39D LYS* 1.3 82.5 - - - +
41D ALA* 1.3 61.4 + - - +
43D GLN* 3.5 0.3 + - - -
44D ALA* 3.0 24.8 + - - +
56D LEU* 3.9 6.7 - - - -
136D GLN* 3.3 22.0 + - - -
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Residues in contact with ALA 41 (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 ASN 3.1 7.8 + - - +
9D ILE* 3.6 37.5 - - + -
36D ILE* 5.3 1.3 - - + -
37D GLY* 3.6 13.5 - - - +
38D GLY 3.3 0.6 + - - -
40D GLY* 1.3 71.3 - - - +
42D ASN* 1.3 61.4 + - - +
45D ILE* 2.8 47.0 + - + +
56D LEU* 3.7 16.1 - - + +
73D ILE* 5.0 0.2 - - + -
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Residues in contact with ASN 42 (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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36D ILE 4.4 0.7 - - - +
37D GLY* 3.4 19.1 - - - -
38D GLY 2.9 18.2 + - - +
41D ALA* 1.3 75.1 - - - +
43D GLN* 1.3 64.5 + - - +
45D ILE* 3.8 3.3 - - - +
46D ILE* 3.1 32.4 + - - +
229D GLY* 4.5 1.8 - - - -
232D ASP* 2.9 33.0 + - + +
270D THR* 3.4 12.0 - - - +
274D PHE* 3.5 29.2 - - + -
501D GOL 3.0 26.3 + - - -
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Residues in contact with GLN 43 (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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5D VAL* 5.1 0.2 - - + -
39D LYS 3.3 15.5 + - - +
40D GLY 4.0 2.0 - - - +
41D ALA 3.3 0.4 - - - -
42D ASN* 1.3 76.0 - - - +
44D ALA* 1.3 63.2 + - - +
47D LEU* 3.1 31.0 + - - +
134D LEU* 3.5 31.4 - - + +
136D GLN* 2.8 32.1 - - - +
161D ASN* 3.1 20.5 + - - +
232D ASP* 2.9 43.5 - - + +
235D LEU* 3.7 17.9 - - + +
236D ALA* 3.6 9.4 - - + +
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Residues in contact with ALA 44 (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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5D VAL* 3.9 19.9 - - + +
40D GLY 3.0 19.0 + - - +
41D ALA 3.8 2.5 - - - +
43D GLN* 1.3 73.2 - - - +
45D ILE* 1.3 66.8 + - - +
47D LEU* 3.4 3.3 + - - +
48D SER* 3.1 23.7 + - - -
54D THR* 3.9 17.7 - - + +
56D LEU* 4.0 15.5 - - + -
78D LEU* 4.0 17.3 - - + +
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Residues in contact with ILE 45 (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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36D ILE* 5.3 3.8 - - + -
41D ALA* 2.8 37.1 + - + +
42D ASN* 3.8 7.6 - - - +
44D ALA* 1.3 73.6 - - - +
46D ILE* 1.3 63.4 + - + +
48D SER* 3.3 5.0 + - - -
49D ARG* 3.0 33.3 + - - +
73D ILE* 3.9 22.0 - - + -
76D GLU* 3.5 32.9 - - + +
78D LEU* 3.8 22.0 - - + -
271D LEU* 3.9 29.2 - - + -
274D PHE* 4.8 7.6 - - + -
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Residues in contact with ILE 46 (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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42D ASN 3.1 17.9 + - - +
45D ILE* 1.3 73.9 - - + +
47D LEU* 1.3 66.2 + - - +
49D ARG* 3.2 8.7 + - - +
50D CYS* 3.1 24.0 + - - -
232D ASP 4.3 2.2 - - - +
233D THR* 3.3 42.0 - - + +
236D ALA* 3.6 18.6 - - + -
237D VAL* 3.7 24.9 - - + -
274D PHE* 3.8 37.9 - - + -
275D PRO* 5.2 2.9 - - + +
280D LEU* 4.7 7.9 - - + -
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Residues in contact with LEU 47 (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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3D VAL* 3.8 28.9 - - + -
5D VAL* 4.4 0.9 - - + -
43D GLN 3.1 24.8 + - - +
44D ALA 3.6 2.5 - - - +
46D ILE* 1.3 78.2 - - - +
48D SER* 1.3 62.7 + - - +
50D CYS* 3.0 17.5 + - - +
52D ILE* 3.2 25.0 + - + +
54D THR* 3.5 19.3 - - + +
134D LEU* 3.9 19.5 - - + -
236D ALA* 3.3 31.0 - - + +
239D LEU* 4.2 13.9 - - + -
240D ALA* 4.0 17.7 - - + +
243D LEU* 4.8 2.7 - - + -
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Residues in contact with SER 48 (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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44D ALA 3.1 16.7 + - - -
45D ILE* 3.8 4.7 - - - -
47D LEU* 1.3 76.0 - - - +
49D ARG* 1.3 58.2 + - - +
51D GLY* 2.9 20.1 + - - -
52D ILE 3.4 16.0 + - - -
53D GLU* 5.5 0.2 - - - -
54D THR* 3.7 4.8 + - - -
77D PRO 4.2 11.9 + - - -
78D LEU* 3.8 22.7 - - - +
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Residues in contact with ARG 49 (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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45D ILE* 3.0 26.5 + - - +
46D ILE* 3.2 8.3 + - - +
48D SER* 1.3 77.1 - - - +
50D CYS* 1.3 59.3 + - - +
51D GLY* 3.1 1.3 + - - -
76D GLU* 2.8 40.4 + - - +
271D LEU* 3.6 19.9 + - - +
274D PHE* 3.3 25.0 + - - +
275D PRO 3.0 29.2 + - - -
276D GLY* 4.1 9.7 - - - -
277D SER* 3.3 41.3 + - - +
280D LEU* 3.5 16.6 - - + +
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Residues in contact with CYS 50 (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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46D ILE 3.1 17.2 + - - -
47D LEU* 3.0 11.0 + - - +
49D ARG* 1.3 76.4 - - - +
51D GLY* 1.3 58.3 + - - +
52D ILE* 3.5 0.8 + - + +
237D VAL* 4.2 14.1 - - - -
240D ALA* 3.5 30.3 - - + -
244D LEU* 3.8 20.3 - - - +
280D LEU* 3.7 29.6 - - - -
284D LEU* 4.0 19.3 - - + +
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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