Contacts of the helix formed by residues 17 - 33 (chain B) in PDB entry 1HQC
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 GLN 17 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14B TYR* 4.2 11.4 - - + +
16B GLY* 1.3 73.5 - - - +
18B GLU* 1.3 60.7 + - - +
19B ARG 3.5 1.6 - - - -
20B LEU* 3.3 22.4 + - + -
21B LYS* 2.9 27.6 + - + +
49B LEU* 5.3 0.2 - - - +
54B LEU* 5.7 1.3 - - + -
164B HIS 5.2 0.2 - - - +
165B LEU* 3.1 29.0 - - + +
166B GLU* 2.5 50.8 + - + +
167B TYR 5.2 0.6 + - - -
168B TYR* 3.5 30.9 + - - +
172B GLU* 3.5 9.3 + - - -
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Residues in contact with GLU 18 (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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16B GLY* 3.3 6.8 + - - +
17B GLN* 1.3 71.7 - - - +
19B ARG* 1.3 69.6 - - - +
21B LYS* 2.7 46.1 + - - +
22B GLN* 2.8 30.6 + - - +
172B GLU* 4.5 12.4 + - - +
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Residues in contact with ARG 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B GLN 3.5 0.6 - - - -
18B GLU* 1.3 77.5 - - - +
20B LEU* 1.3 57.6 + - - +
22B GLN* 3.1 25.2 + - - +
23B LYS* 2.8 43.3 + - + +
166B GLU* 6.5 0.7 - - + -
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Residues in contact with LEU 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B GLN* 3.3 19.2 + - + +
18B GLU 3.1 0.4 - - - -
19B ARG* 1.3 75.9 - - - +
21B LYS* 1.3 55.8 + - + +
23B LYS* 3.2 6.0 + - + -
24B LEU* 2.7 53.4 + - + +
43B LEU* 4.4 7.0 - - + -
54B LEU* 3.4 30.5 - - + -
163B GLU* 3.4 36.8 - - + -
164B HIS 4.0 10.3 - - - +
165B LEU* 3.9 26.0 - - + -
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Residues in contact with LYS 21 (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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11B LEU* 3.0 47.6 + - + +
12B ASP* 3.6 14.8 + - - +
14B TYR* 3.0 28.0 + - + +
16B GLY 3.3 17.4 - - - +
17B GLN* 2.9 16.3 + - + +
18B GLU* 2.7 44.0 + - - +
20B LEU* 1.3 72.1 - - + +
22B GLN* 1.3 52.3 + - + +
24B LEU* 3.5 4.0 - - - +
25B ARG* 2.7 47.7 + - - +
54B LEU* 5.4 2.7 - - + -
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Residues in contact with GLN 22 (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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18B GLU* 2.8 33.8 + - + +
19B ARG* 3.3 30.9 - - - +
21B LYS* 1.3 72.2 - - + +
23B LYS* 1.3 66.0 + - - +
25B ARG* 2.8 22.8 + - - +
26B VAL* 3.0 16.6 + - + +
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Residues in contact with LYS 23 (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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19B ARG* 2.8 29.5 + - + +
20B LEU* 3.5 14.6 - - + +
22B GLN* 1.3 73.4 - - - +
24B LEU* 1.3 56.6 + - - +
26B VAL* 3.3 8.1 + - - +
27B TYR* 2.7 52.7 + - + -
163B GLU* 3.3 40.5 + - + +
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Residues in contact with LEU 24 (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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11B LEU* 4.1 15.3 - - + -
20B LEU* 2.7 40.9 + - + +
21B LYS 3.5 3.1 - - - +
23B LYS* 1.3 69.3 - - - +
25B ARG* 1.3 68.3 + - - +
27B TYR* 2.8 14.1 + - + +
28B LEU* 2.8 31.7 + - + +
38B LEU* 5.5 4.7 - - + -
41B LEU* 4.0 23.6 - - + -
43B LEU* 5.2 0.7 - - + -
54B LEU* 3.6 24.5 - - + -
58B ILE* 3.6 38.6 - - + -
161B ILE* 5.2 2.5 - - + -
163B GLU* 5.6 0.2 - - + -
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Residues in contact with ARG 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 4.0 36.6 + - - +
12B ASP* 2.6 39.4 + - - +
21B LYS* 2.7 28.8 + - - +
22B GLN* 2.8 14.6 + - - +
24B LEU* 1.3 71.1 - - - +
26B VAL* 1.3 65.0 + - + +
28B LEU* 4.4 2.9 - - - -
29B GLU* 3.0 53.0 + - + +
61B GLU* 4.9 6.6 + - - -
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Residues in contact with VAL 26 (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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22B GLN* 3.0 14.7 + - + +
23B LYS* 3.5 11.4 - - - +
24B LEU 3.0 0.2 - - - -
25B ARG* 1.3 78.6 - - + +
27B TYR* 1.3 67.4 + - + +
29B GLU* 5.4 0.9 - - - -
30B ALA* 2.8 34.1 + - + +
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Residues in contact with TYR 27 (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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23B LYS* 2.7 52.2 + - + -
24B LEU* 2.8 15.9 + - + +
26B VAL* 1.3 79.7 - - + +
28B LEU* 1.3 63.1 + - + +
30B ALA* 4.2 2.8 - - - +
31B ALA* 3.0 25.3 + - - +
38B LEU* 4.5 14.9 - - + +
39B GLU* 5.3 4.0 - - - -
161B ILE* 3.2 52.3 - - + +
163B GLU* 3.9 12.8 + - + -
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Residues in contact with LEU 28 (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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11B LEU* 3.6 30.7 - - + -
24B LEU* 2.8 23.2 + - + +
25B ARG* 3.5 4.5 - - - +
27B TYR* 1.3 74.2 - - + +
29B GLU* 1.3 64.4 + - - +
30B ALA 3.0 1.3 - - - -
31B ALA* 2.2 35.5 + - - -
32B LYS* 2.7 16.7 + - + -
38B LEU* 3.7 22.7 - - + -
58B ILE* 4.1 12.1 - - + +
61B GLU* 3.8 23.1 - - + +
62B LEU* 3.5 33.7 - - + -
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Residues in contact with GLU 29 (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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25B ARG* 3.0 47.7 + - + +
26B VAL* 4.9 1.3 - - - +
28B LEU* 1.3 80.2 - - - +
30B ALA* 1.3 65.0 - - - +
31B ALA 2.8 1.2 + - - -
32B LYS* 2.9 39.9 + - + +
33B ALA* 3.0 24.0 + - - +
61B GLU* 4.6 5.2 - - - +
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Residues in contact with ALA 30 (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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26B VAL* 2.8 26.0 + - + +
27B TYR* 4.2 4.7 - - - +
28B LEU 2.8 1.2 + - - -
29B GLU* 1.3 77.7 - - - +
31B ALA* 1.3 49.9 + - - +
33B ALA* 3.4 7.9 - - - +
34B ARG* 2.5 47.2 + - - +
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Residues in contact with ALA 31 (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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27B TYR 3.0 20.0 - - - +
28B LEU* 2.2 25.6 + - - +
30B ALA* 1.3 68.9 - - - +
32B LYS* 1.3 59.2 + - - +
33B ALA 2.9 5.4 - - - -
34B ARG* 3.1 15.4 + - + +
35B LYS 2.6 29.9 - - - +
36B GLU* 5.2 1.3 - - - -
37B PRO 5.6 1.1 - - - -
38B LEU* 5.0 16.8 - - - +
62B LEU* 5.1 5.2 - - + -
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Residues in contact with LYS 32 (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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28B LEU* 2.7 19.5 + - + +
29B GLU* 2.9 39.3 + - - +
31B ALA* 1.3 72.5 - - - +
33B ALA* 1.3 61.5 + - - +
34B ARG 3.5 5.5 + - - +
36B GLU* 3.5 26.1 - - - +
61B GLU* 3.7 39.5 + - - +
62B LEU* 4.0 23.5 - - + +
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Residues in contact with ALA 33 (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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29B GLU 3.0 16.8 + - - +
30B ALA* 3.4 12.1 - - - +
31B ALA 2.9 0.2 - - - -
32B LYS* 1.3 79.6 - - - +
34B ARG* 1.3 64.5 + - - +
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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