Contacts of the helix formed by residues 15 - 27 (chain D) in PDB entry 3KHU
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 VAL 15 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14D TYR* 1.3 79.3 - - + +
16D GLY* 1.3 66.3 + - - +
18D PRO* 4.5 0.2 - - - +
19D THR* 2.7 36.2 + - - +
88D SER* 3.8 3.8 - - - +
129D LYS* 3.7 25.8 - - + +
130D SER* 3.9 3.6 - - - +
161D GLN* 3.4 45.1 - - + +
163D LEU* 4.3 8.2 - - + +
502D UPG 3.1 38.8 + - - +
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Residues in contact with GLY 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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9D CYS* 4.0 6.0 - - - -
11D GLY 3.5 16.1 + - - -
13D GLY 3.6 4.2 + - - -
15D VAL* 1.3 81.3 - - - +
17D GLY* 1.3 62.0 + - - +
19D THR* 4.8 2.0 - - - -
20D CYS* 3.0 30.7 + - - +
34D VAL* 4.7 1.5 - - - +
88D SER* 3.1 23.3 + - - -
129D LYS* 4.9 1.3 - - - -
502D UPG 4.2 0.6 + - - -
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Residues in contact with GLY 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D GLY 4.3 0.8 + - - -
12D ALA* 4.8 0.2 - - - -
13D GLY 3.2 9.7 + - - +
16D GLY* 1.3 72.5 - - - +
18D PRO* 1.3 64.3 - - - +
20D CYS* 3.7 0.5 - - - +
21D SER* 2.6 40.7 + - - -
34D VAL* 4.7 11.8 - - - +
45D TRP* 3.7 24.0 - - - -
71D PHE* 4.7 2.8 - - - -
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Residues in contact with PRO 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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13D GLY 3.4 6.1 - - - +
14D TYR* 3.1 29.8 - - - +
15D VAL 3.8 0.7 - - - +
17D GLY* 1.3 87.6 - - - +
19D THR* 1.3 63.5 + - - +
21D SER* 3.5 1.2 - - - -
22D VAL* 3.0 27.5 + - - +
45D TRP* 3.9 6.3 - - + -
52D ILE* 4.8 8.5 - - + -
54D GLU* 5.3 1.3 - - + -
57D LEU* 4.0 33.9 - - + -
163D LEU* 4.7 4.9 - - + -
168D ALA* 4.8 11.7 - - + -
169D ILE* 4.9 2.7 - - + -
172D LEU* 3.7 14.6 - - + -
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Residues in contact with THR 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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15D VAL* 2.7 31.5 + - - +
16D GLY 4.2 0.4 - - - -
18D PRO* 1.3 79.1 - - - +
20D CYS* 1.3 59.4 + - - +
22D VAL* 3.3 3.3 + - - +
23D ILE* 3.1 39.9 + - + +
129D LYS* 3.9 24.4 - - + +
161D GLN* 4.8 4.7 - - + +
163D LEU* 4.0 6.9 - - - +
172D LEU* 3.8 28.8 - - + +
199D TYR* 4.6 12.6 - - + +
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Residues in contact with CYS 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D ILE* 4.6 0.9 - - - -
9D CYS* 3.3 30.7 - - - -
16D GLY 3.0 18.1 + - - +
19D THR* 1.3 76.1 - - - +
21D SER* 1.3 64.9 + - - +
23D ILE* 3.8 8.2 - - - +
24D ALA* 3.2 23.0 + - - +
32D VAL* 3.7 19.9 - - + +
34D VAL* 3.8 19.7 - - + -
69D LEU* 4.1 2.3 - - - +
86D PHE* 3.7 26.5 - - - -
129D LYS* 5.0 4.3 - - - -
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Residues in contact with SER 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D GLY 2.6 27.1 + - - -
18D PRO* 3.5 7.6 - - - -
20D CYS* 1.3 74.5 - - - +
22D VAL* 1.3 64.4 + - - +
24D ALA* 3.3 3.8 + - - +
25D HIS* 3.0 22.3 + - - +
45D TRP* 4.6 0.2 - - - -
57D LEU* 4.4 2.2 - - - +
60D VAL* 3.7 12.2 - - - +
61D VAL* 3.7 21.2 - - - +
64D CYS* 4.1 2.4 - - - -
69D LEU* 3.7 26.5 - - - +
71D PHE* 3.8 8.8 - - - -
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Residues in contact with VAL 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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18D PRO 3.0 18.7 + - - +
19D THR 3.8 4.3 - - - +
21D SER* 1.3 75.4 - - - +
23D ILE* 1.3 65.4 + - - +
25D HIS* 3.2 3.7 + - + +
26D MET* 3.0 36.8 + - + +
60D VAL* 4.2 13.9 - - + -
169D ILE* 3.9 25.4 - - + -
172D LEU* 3.9 30.5 - - + +
173D LYS* 4.5 15.7 - - + -
202D TRP* 4.2 17.5 - - + +
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Residues in contact with ILE 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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7D ILE* 3.9 18.8 - - + -
19D THR* 3.1 31.7 + - + +
20D CYS* 3.8 13.9 - - - +
21D SER 3.3 0.2 - - - -
22D VAL* 1.3 75.4 - - - +
24D ALA* 1.3 52.3 + - - +
26D MET 3.1 1.7 + - - -
27D CYS* 2.8 42.1 + - + +
30D ILE* 5.3 0.4 - - + -
32D VAL* 4.4 6.1 - - + -
86D PHE* 3.8 33.4 - - + -
198D VAL* 3.9 26.9 - - + -
199D TYR* 4.8 7.9 - - + +
202D TRP* 3.9 24.0 - - + -
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Residues in contact with ALA 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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20D CYS 3.2 15.5 + - - +
21D SER 3.6 4.5 - - - +
22D VAL 3.3 0.2 - - - -
23D ILE* 1.3 78.1 - - - +
25D HIS* 1.3 61.7 + - - +
27D CYS 3.4 10.2 + - - +
28D PRO* 3.8 1.9 - - - +
32D VAL* 3.7 17.0 - - + -
64D CYS* 3.9 5.7 - - - +
68D ASN* 2.9 35.5 + - - +
69D LEU* 3.8 26.0 - - + -
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Residues in contact with HIS 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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21D SER 3.0 13.7 + - - +
22D VAL* 3.2 9.2 + - - +
24D ALA* 1.3 76.9 - - - +
26D MET* 1.3 85.8 + - + +
27D CYS 3.8 0.2 + - - -
28D PRO* 4.8 6.4 - - - +
60D VAL* 3.9 19.7 + - + -
63D SER* 2.9 31.6 + - - -
64D CYS* 3.7 10.4 - - - +
173D LYS* 4.3 19.3 + - - -
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Residues in contact with MET 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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22D VAL* 3.0 23.1 + - + +
23D ILE 3.9 0.7 - - - +
25D HIS* 1.3 91.2 - - + +
27D CYS* 1.3 61.6 + - - +
28D PRO* 3.6 9.2 - - - +
173D LYS* 3.6 45.5 - - + +
201D HIS* 3.8 15.1 - - - +
202D TRP* 3.5 56.5 - - + -
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Residues in contact with CYS 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D ILE* 2.8 18.6 + - + +
24D ALA* 3.4 3.7 + - - +
26D MET* 1.3 82.3 - - - +
28D PRO* 1.3 67.2 - - - +
29D GLU* 3.2 8.1 - - - +
30D ILE* 3.0 32.2 + - + +
68D ASN* 3.0 12.5 + - - -
198D VAL* 3.7 23.1 - - - -
201D HIS* 3.7 29.2 - - + -
202D TRP* 4.0 10.5 - - - -
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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