Contacts of the helix formed by residues 18 - 32 (chain B) in PDB entry 4ZDR
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 ARG 18 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A ALA 6.0 0.2 - - - -
55A ARG* 4.3 13.5 - - - +
58A SER* 3.5 25.1 + - - +
82A TYR* 3.1 24.8 + - - +
85A LYS* 6.0 0.6 - - - +
86A ILE* 4.0 22.6 - - - +
89A GLU* 2.3 40.0 + - - -
13B ALA* 3.0 13.2 + - - +
16B ALA* 3.5 16.6 - - - +
17B GLU* 1.3 76.3 - - - +
19B TYR* 1.3 61.9 + - - +
20B ASP* 3.1 7.9 + - + -
21B ASP* 3.0 31.5 + - + +
22B MET 3.2 15.1 + - - -
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Residues in contact with TYR 19 (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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14B GLU* 4.1 20.6 + - + +
17B GLU* 3.7 42.9 + - + -
18B ARG* 1.3 73.3 - - - +
20B ASP* 1.3 61.1 + - - +
22B MET* 3.7 25.9 - - - +
23B ALA* 3.0 19.6 + - - +
46B VAL* 4.3 9.2 - - + -
47B ALA* 4.0 5.0 - - - +
50B ASN* 3.3 56.4 + - + -
51B VAL* 3.0 24.2 - - + +
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Residues in contact with ASP 20 (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 ARG* 3.1 1.9 + - + -
19B TYR* 1.3 75.5 - - - +
21B ASP* 1.3 69.2 + - - +
23B ALA* 3.0 5.1 + - - +
24B ALA* 3.0 22.2 + - - +
51B VAL* 3.2 22.1 - - - +
55B ARG* 3.5 31.4 + - - -
303B TME 4.7 5.6 - - - +
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Residues in contact with ASP 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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82A TYR* 2.7 37.8 + - + +
9B LYS* 5.1 9.6 - - - -
13B ALA* 4.1 3.4 - - + -
18B ARG* 3.0 35.8 + - - +
20B ASP* 1.3 77.8 - - - +
22B MET* 1.3 57.3 + - - +
24B ALA* 3.1 9.4 + - - +
25B CYS* 2.9 32.9 + - - -
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Residues in contact with MET 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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10B ALA* 3.5 18.6 - - + +
13B ALA* 3.6 15.5 - - + +
14B GLU* 3.7 26.5 - - + -
18B ARG 3.2 4.8 + - - +
19B TYR* 3.7 21.8 - - - +
20B ASP 3.1 1.0 - - - -
21B ASP* 1.3 80.3 - - - +
23B ALA* 1.3 57.2 + - - +
25B CYS* 3.3 5.5 + - - +
26B MET* 3.1 29.6 + - + +
43B LEU* 3.1 52.3 - - + +
46B VAL* 3.7 19.3 - - + -
47B ALA* 3.6 13.7 - - + -
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Residues in contact with ALA 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 TYR 3.0 17.2 + - - +
20B ASP* 3.0 5.6 + - - +
22B MET* 1.3 74.2 - - - +
24B ALA* 1.3 60.0 + - - +
26B MET* 4.5 1.3 - - - +
27B LYS* 2.9 33.3 + - - +
47B ALA* 3.7 12.1 - - + +
48B TYR* 3.7 36.0 + - + +
51B VAL* 4.1 11.0 - - + -
303B TME 4.7 5.8 - - + -
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Residues in contact with ALA 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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20B ASP 3.0 12.3 + - - +
21B ASP* 3.1 13.7 + - - +
23B ALA* 1.3 77.7 - - - +
25B CYS* 1.3 62.4 + - - +
27B LYS* 3.7 7.1 - - - +
28B SER* 3.0 24.3 + - - -
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Residues in contact with CYS 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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6B LEU* 3.7 42.5 - - + +
9B LYS* 4.0 32.3 - - - -
10B ALA* 4.1 12.8 - - + -
21B ASP 2.9 20.8 + - - -
22B MET 3.7 6.7 - - - +
23B ALA 3.3 0.2 - - - -
24B ALA* 1.3 78.2 - - - +
26B MET* 1.3 59.4 + - - +
28B SER* 3.4 4.0 - - - -
29B VAL* 2.9 31.1 + - - +
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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
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7B VAL* 4.2 15.7 - - + -
10B ALA* 3.7 23.1 - - + -
22B MET* 3.1 17.1 + - + +
23B ALA* 4.3 2.2 - - - +
25B CYS* 1.3 76.5 - - - +
27B LYS* 1.3 57.8 + - - +
29B VAL* 3.6 16.9 - - + +
30B THR* 2.7 38.5 + - - -
36B LEU* 5.0 2.9 - - + -
40B GLU* 3.4 44.6 - - + +
43B LEU* 3.9 13.5 - - + +
44B LEU* 3.6 36.8 - - + +
47B ALA* 5.0 0.4 - - + -
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Residues in contact with LYS 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 ALA 2.9 20.3 + - - +
24B ALA* 3.7 6.7 - - - +
26B MET* 1.3 73.2 - - - +
28B SER* 1.3 60.7 + - - +
30B THR* 3.2 6.3 + - - -
31B GLU* 2.9 56.6 + - - +
44B LEU* 4.4 1.7 - - - +
48B TYR* 3.8 16.4 - - + +
96B ASP* 3.5 30.8 + - - +
100B LEU* 3.7 27.6 - - + -
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Residues in contact with SER 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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0B LEU* 5.9 2.8 - - - +
6B LEU* 3.8 24.8 - - - +
24B ALA 3.0 13.3 + - - -
25B CYS 3.4 9.6 - - - -
27B LYS* 1.3 76.4 - - - +
29B VAL* 1.3 63.5 + - - +
31B GLU* 3.2 23.3 + - - +
32B GLN* 3.3 19.8 + - - +
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Residues in contact with VAL 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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3B LYS* 3.9 21.8 - - + +
6B LEU* 3.5 29.1 - - + +
7B VAL* 4.0 16.4 - - + +
25B CYS 2.9 21.2 + - - +
26B MET* 3.3 18.1 + - + +
28B SER* 1.3 73.1 - - - +
30B THR* 1.3 65.0 + - - +
32B GLN* 3.2 21.2 + - - +
33B GLY 4.4 0.9 + - - -
34B ALA* 5.3 2.6 + - - +
36B LEU* 3.8 20.8 - - + +
40B GLU* 4.3 10.8 - - - +
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Residues in contact with THR 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 2.7 27.3 + - - -
27B LYS* 3.5 5.4 - - - -
29B VAL* 1.3 72.7 - - - +
31B GLU* 1.3 63.1 + - - +
33B GLY* 3.1 12.8 + - - -
34B ALA 4.4 6.6 - - - +
36B LEU* 3.6 24.9 - - + +
44B LEU* 3.7 11.3 - - - +
100B LEU* 3.9 20.0 - - + -
104B PHE* 3.7 17.8 - - + +
105B LEU* 3.6 37.2 - - + -
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Residues in contact with GLU 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 LYS* 2.9 47.2 + - - +
28B SER* 3.2 16.2 + - - +
30B THR* 1.3 72.0 - - - +
32B GLN* 1.3 58.2 + - + +
33B GLY* 2.9 11.0 + - - -
100B LEU* 4.1 12.8 - - + +
104B PHE* 3.4 29.9 - - + -
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Residues in contact with GLN 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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0B LEU* 5.4 4.8 - - - +
1B MET 4.3 7.9 + - - -
2B ASP* 4.9 1.6 - - - +
3B LYS* 3.7 27.9 + - - +
6B LEU* 3.7 22.8 - - - +
28B SER* 3.5 16.0 + - - +
29B VAL* 3.2 11.8 + - - +
30B THR 3.2 1.6 - - - -
31B GLU* 1.3 75.9 - - + +
33B GLY* 1.3 55.4 + - - +
34B ALA* 3.3 11.2 + - + +
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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