Contacts of the helix formed by residues 24 - 37 (chain B) in PDB entry 2HAN
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 CYS 24 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7B CYS* 3.4 10.0 - - + +
10B CYS* 3.7 0.7 - - - -
12B ASP* 4.1 9.9 - - + +
13B ARG 3.3 24.0 - - - +
14B ALA* 4.0 0.9 - - - +
15B SER* 4.0 3.4 - - - +
23B THR* 1.3 78.0 - - - +
25B GLU* 1.3 60.5 + - - +
26B GLY 3.6 6.3 - - - +
27B CYS* 3.3 18.5 + - - -
28B LYS* 3.0 28.2 + - - +
56B ARG* 3.7 18.4 - - - -
353B ZN 2.3 36.1 - - - -
14C C 5.8 0.7 - - - +
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Residues in contact with GLU 25 (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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13B ARG* 4.9 1.9 + - - +
15B SER* 2.8 31.7 + - - +
18B HIS* 3.8 3.6 - - - -
24B CYS* 1.3 71.1 - - - +
26B GLY* 1.3 66.2 + - - +
28B LYS* 3.0 41.3 + - - +
29B GLY* 3.1 20.3 + - - -
13C G 4.4 4.0 - - - +
14C C 3.9 36.7 + - + +
15C A 3.3 25.7 + - - +
16C C 4.5 3.8 + - - -
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Residues in contact with GLY 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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24B CYS* 3.3 8.0 - - - +
25B GLU* 1.3 79.2 - - - +
27B CYS* 1.3 56.3 - - - +
29B GLY* 3.8 0.5 - - - -
30B PHE* 2.9 26.0 + - - +
33B ARG* 5.0 0.9 + - - -
56B ARG* 5.1 2.2 - - - -
63B ARG* 3.1 13.4 + - - -
13C G 3.7 39.7 + - - +
14C C 4.4 2.6 + - - -
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Residues in contact with CYS 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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7B CYS* 4.0 6.7 - - - -
9B VAL* 3.7 27.6 - - + -
10B CYS* 3.9 5.2 - - - -
23B THR* 4.3 6.5 - - + -
24B CYS* 3.3 6.6 - - - +
26B GLY* 1.3 71.5 - - - +
28B LYS* 1.3 59.9 + - - +
30B PHE* 3.8 2.3 - - - +
31B PHE* 2.8 34.4 + - - +
63B ARG* 3.2 31.5 - - - +
67B CYS* 4.5 4.3 - - - -
72B MET* 4.0 2.9 - - - +
353B ZN 2.3 35.0 - - - -
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Residues in contact with LYS 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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18B HIS* 3.6 37.8 - - + +
19B TYR* 4.1 13.5 - - + -
23B THR* 4.5 0.6 + - - -
24B CYS 3.0 17.6 + - - +
25B GLU* 3.0 40.8 + - - +
27B CYS* 1.3 76.8 - - - +
29B GLY* 1.3 58.1 + - - +
31B PHE* 3.6 1.9 - - - +
32B ARG* 2.9 32.4 + - + +
72B MET* 4.1 13.8 - - - +
16C C 4.3 2.6 - - - +
5D A 4.0 13.6 + - - +
6D G 2.7 44.4 + - - -
7D T 4.7 5.8 - - - -
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Residues in contact with GLY 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 GLU 3.1 14.1 + - - -
26B GLY 3.8 2.0 - - - -
28B LYS* 1.3 76.7 - - - +
30B PHE* 1.3 60.8 + - - +
32B ARG* 3.8 11.8 - - - +
33B ARG* 2.9 44.9 + - - +
13C G 5.3 8.1 - - - -
14C C 6.0 2.7 - - - -
7D T 6.2 1.1 - - - -
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Residues in contact with PHE 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 GLY 2.9 18.3 + - - +
27B CYS 3.8 1.6 - - - +
29B GLY* 1.3 75.9 - - - +
31B PHE* 1.3 58.9 + - - +
33B ARG* 3.6 14.9 - - - +
34B SER* 2.8 51.7 + - - -
41B TYR* 3.7 17.3 - + - -
60B GLN* 3.5 41.1 - - + -
63B ARG* 3.5 43.7 - - + +
64B LEU* 3.5 29.4 - - + -
67B CYS* 4.1 9.2 - - - -
12C T 3.6 18.4 - - - -
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Residues in contact with PHE 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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19B TYR* 3.8 16.2 - + + -
27B CYS 2.8 19.3 + - - +
28B LYS 3.6 1.1 - - - +
30B PHE* 1.3 80.1 - - - +
32B ARG* 1.3 65.3 + - - +
34B SER* 3.3 3.5 + - - -
35B VAL* 2.9 38.6 + - + +
64B LEU* 3.9 11.4 - - + -
67B CYS* 3.6 21.8 - - + -
68B LEU* 3.6 23.3 - - + -
72B MET* 3.5 52.0 - - + -
73B ARG 3.9 9.2 - - - -
74B PRO* 3.7 15.5 - - + -
77B VAL* 3.7 20.6 - - + -
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Residues in contact with ARG 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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19B TYR* 3.4 26.2 - - + +
28B LYS* 2.9 19.9 + - + +
29B GLY* 3.8 9.2 + - - +
31B PHE* 1.3 78.3 - - - +
33B ARG* 1.3 81.5 + - - +
35B VAL* 3.8 0.7 - - - +
36B THR* 2.8 54.2 + - + +
77B VAL* 3.8 23.1 - - + -
78B VAL* 5.5 2.2 - - - -
6D G 4.3 16.2 - - - -
7D T 3.2 46.4 + - - +
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Residues in contact with ARG 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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26B GLY 5.0 0.4 + - - -
29B GLY* 2.9 22.2 + - - +
30B PHE* 3.6 25.6 - - - +
32B ARG* 1.3 93.1 - - - +
34B SER* 1.3 66.2 + - - +
36B THR* 3.7 6.7 - - - -
37B LYS* 3.1 48.7 + - + +
41B TYR* 5.5 1.4 + - - +
11C A 3.6 13.3 - - - +
12C T 2.7 82.7 + - - +
13C G 4.6 9.3 + - - -
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Residues in contact with SER 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B PHE* 2.8 29.5 + - - -
31B PHE 3.6 4.5 - - - -
33B ARG* 1.3 77.0 - - - +
35B VAL* 1.3 57.8 + - - +
37B LYS* 4.7 0.2 - - - +
38B SER* 3.0 7.4 + - - -
39B ALA* 3.0 31.3 + - - +
41B TYR* 2.7 40.6 + - - -
64B LEU* 4.1 22.7 - - - -
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Residues in contact with VAL 35 (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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31B PHE* 2.9 50.5 + - + +
32B ARG 3.8 2.7 - - - +
34B SER* 1.3 77.8 - - - +
36B THR* 1.3 68.6 + - - +
38B SER* 3.0 18.6 + - - +
64B LEU* 5.2 3.4 - - + -
68B LEU* 5.9 0.2 - - + -
74B PRO* 3.8 24.0 - - + +
77B VAL* 3.7 26.7 - - + +
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Residues in contact with THR 36 (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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32B ARG* 2.8 45.5 + - + +
33B ARG* 3.4 10.4 + - - -
35B VAL* 1.3 73.9 - - - +
37B LYS* 1.3 63.2 + - - +
38B SER* 3.7 3.1 + - - -
77B VAL* 3.6 20.2 - - + -
78B VAL* 4.3 14.8 - - + -
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Residues in contact with LYS 37 (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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33B ARG* 3.1 37.7 + - + +
36B THR* 1.3 78.9 - - - +
38B SER* 1.3 69.4 + - - +
39B ALA* 3.1 20.3 + - + +
41B TYR* 4.1 14.7 + - - -
60B GLN* 6.1 0.8 - - - +
11C A 4.6 23.6 + - - +
12C T 5.7 0.4 + - - -
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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