Contacts of the helix formed by residues 21 - 33 (chain B) in PDB entry 4RHW
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 LYS 21 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19B ASP 3.7 1.2 + - - -
20B ILE* 1.3 69.4 - - - +
22B THR* 1.3 64.7 + - - +
23B SER* 3.3 7.2 + - - +
24B TYR* 3.1 56.3 + - + +
25B ILE* 3.5 13.3 + - - +
49B GLN* 5.3 0.4 - - - -
80B TYR* 3.1 18.6 + - - +
101B SO4 3.3 33.2 - - - +
48E SER* 6.0 1.0 + - - -
53E ASP* 4.8 11.9 + - - -
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Residues in contact with THR 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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20B ILE* 4.1 13.0 - - + +
21B LYS* 1.3 72.5 - - - +
23B SER* 1.3 59.4 + - - +
25B ILE* 3.2 7.4 + - - +
26B MET* 2.8 48.1 + - - +
43B VAL* 4.5 3.1 - - - -
49B GLN 4.3 0.7 - - - +
52B ARG* 3.7 12.5 + - - +
53B ALA* 3.2 46.7 - - + +
56B LEU* 4.6 7.9 - - + -
101B SO4 2.7 25.9 + - - +
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Residues in contact with SER 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LYS* 3.6 9.2 + - - -
22B THR* 1.3 78.3 + - - +
24B TYR* 1.3 76.1 + - - +
26B MET* 3.9 13.3 - - - +
27B ASP* 3.0 28.1 + - - +
40B GLU* 5.3 0.6 - - - +
44B ARG* 5.8 4.3 - - - -
101B SO4 2.9 20.7 + - - -
53E ASP* 4.6 1.7 + - - -
56E ARG* 3.7 29.2 + - - +
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Residues in contact with TYR 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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21B LYS* 3.1 48.5 + - + +
22B THR 3.3 0.6 - - - -
23B SER* 1.3 83.1 - - - +
25B ILE* 1.3 64.4 + - + +
27B ASP* 3.1 18.6 + - - +
28B HIS* 3.2 20.2 - - - -
78B GLU* 3.3 36.8 - - + +
80B TYR* 5.7 3.4 - + + +
52E ARG* 4.0 41.0 + - - +
53E ASP* 5.8 0.2 - - - -
56E ARG* 4.7 1.3 - - - -
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Residues in contact with ILE 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ILE* 4.5 16.8 - - + -
21B LYS 3.5 11.8 + - - +
22B THR* 3.2 7.4 + - - +
24B TYR* 1.3 76.1 - - + +
26B MET* 1.3 62.0 + - - +
28B HIS* 3.3 7.0 + - - +
29B MET* 3.2 23.0 + - - +
56B LEU* 4.1 13.2 - - + -
71B PHE* 3.8 30.7 - - + -
74B ALA* 3.6 39.9 - - + +
75B LEU* 3.7 19.5 - - + +
78B GLU* 4.6 3.6 - - + -
80B TYR* 4.2 12.8 - - + -
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Residues in contact with MET 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B THR* 2.8 35.1 + - - +
23B SER* 4.0 8.7 - - - +
25B ILE* 1.3 69.6 - - - +
27B ASP* 1.3 66.8 + - - +
29B MET* 3.2 4.1 + - - +
30B ILE* 2.9 29.9 + - - +
35B LEU* 3.5 30.5 - - + -
40B GLU* 4.0 20.9 - - + +
43B VAL* 3.3 47.6 - - + -
44B ARG* 4.1 20.2 - - + +
52B ARG* 5.5 0.2 - - + -
56B LEU* 4.0 17.3 - - + -
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Residues in contact with ASP 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B SER 3.0 18.0 + - - +
24B TYR* 3.1 10.2 + - - +
26B MET* 1.3 75.8 - - - +
28B HIS* 1.3 61.6 + - - +
30B ILE 3.5 0.2 + - - -
31B SER* 3.1 26.0 + - - -
40B GLU* 4.4 0.3 - - - +
13E ARG* 3.0 28.4 + - + +
14E LEU* 3.4 10.1 - - + -
17E VAL* 3.6 10.3 - - - +
52E ARG* 2.8 29.9 + - - +
56E ARG* 2.8 39.3 + - - -
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Residues in contact with HIS 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B TYR 3.2 23.3 + - - -
25B ILE 3.3 7.7 + - - +
26B MET 3.2 0.2 - - - -
27B ASP* 1.3 80.2 - - - +
29B MET* 1.3 56.6 + - - +
31B SER* 3.2 3.2 + - - -
32B ASP* 2.9 40.6 + - - +
74B ALA* 3.7 24.0 + - + -
77B HIS* 4.0 29.7 + - + +
78B GLU* 2.7 36.7 + - + +
14E LEU* 3.2 31.1 - - + +
18E GLU* 5.6 0.7 - - - -
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Residues in contact with MET 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ILE* 3.2 17.9 + - + +
26B MET* 3.2 9.8 + - - +
28B HIS* 1.3 72.7 - - - +
30B ILE* 1.3 64.0 + - - +
32B ASP 3.4 0.5 + - - -
33B GLY 3.0 3.6 + - - -
34B PHE* 2.9 51.9 + - + +
35B LEU* 3.6 18.8 + - + +
56B LEU* 4.6 8.3 - - - -
60B ILE* 3.9 35.0 - - + -
63B LYS* 4.9 1.8 - - + -
67B SER* 3.8 25.6 - - - +
70B SER* 3.5 21.5 - - - +
71B PHE* 4.2 16.4 - - - +
74B ALA* 5.0 0.9 - - + -
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Residues in contact with ILE 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 MET 2.9 21.2 + - - +
27B ASP 3.6 4.5 - - - +
29B MET* 1.3 72.6 - - - +
31B SER* 1.3 67.6 + - - +
33B GLY* 2.9 14.2 + - - -
35B LEU* 3.6 27.6 - - + +
36B THR 3.8 20.2 - - - +
37B ILE* 4.0 9.2 - - + +
40B GLU* 3.8 22.9 - - + +
10E ARG* 3.6 37.7 - - + +
13E ARG* 3.9 30.7 - - + +
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Residues in contact with SER 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ASP 3.1 9.6 + - - -
28B HIS 3.4 8.3 - - - -
30B ILE* 1.3 80.8 - - - +
32B ASP* 1.3 64.5 + - - +
33B GLY* 3.3 1.0 + - - -
10E ARG 3.2 11.2 + - - -
11E ARG* 3.8 24.0 + - - +
13E ARG* 3.3 4.9 + - - +
14E LEU* 3.1 40.1 + - - +
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Residues in contact with ASP 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B HIS* 2.9 23.2 + - - +
29B MET 3.8 1.1 - - - +
30B ILE 3.2 0.4 - - - -
31B SER* 1.3 79.2 - - - +
33B GLY* 1.3 58.1 + - - +
34B PHE* 3.4 26.6 - - + -
70B SER* 2.8 39.3 + - - +
73B ASN* 5.1 5.5 + - - +
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Residues in contact with GLY 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 MET 3.0 0.4 + - - -
30B ILE 2.9 16.5 + - - -
31B SER 3.2 1.0 + - - -
32B ASP* 1.3 79.2 - - - +
34B PHE* 1.3 67.2 + - - +
35B LEU 3.5 6.4 + - - -
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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