Contacts of the helix formed by residues 32 - 45 (chain D) in PDB entry 1RZR
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 SER 32 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30D LYS* 2.6 34.1 + - - +
31D PRO* 1.3 74.8 - - - +
33D THR* 1.3 67.6 + - - -
35D LYS* 3.2 2.8 + - - +
36D LYS* 2.9 25.5 + - - +
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Residues in contact with THR 33 (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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701B T 3.0 28.0 + - - +
14D VAL* 4.0 27.8 - - + +
18D THR* 5.0 8.7 - - + -
22D VAL* 4.9 3.1 - - + -
29D VAL* 3.5 19.5 - - + -
30D LYS* 2.8 9.4 + - - +
32D SER* 1.3 75.3 + - - +
34D ARG* 1.3 55.1 + - - +
35D LYS 2.7 12.1 + - - -
36D LYS* 3.0 17.2 + - - +
37D VAL* 3.2 20.7 + - + +
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Residues in contact with ARG 34 (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 ARG 4.1 4.0 + - - -
22D VAL* 3.6 21.9 + - + +
25D GLY* 4.1 8.7 - - - -
26D ASN 2.6 44.0 + - - +
27D PRO* 5.7 0.6 - - - +
29D VAL* 3.2 43.4 + - + +
30D LYS 2.7 23.1 + - - +
31D PRO* 4.1 9.0 - - + +
33D THR* 1.3 72.8 - - - +
35D LYS* 1.3 60.1 + - + +
37D VAL* 4.3 0.2 - - - -
38D LEU* 2.7 37.3 + - + +
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Residues in contact with LYS 35 (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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31D PRO* 3.4 19.4 + - + +
32D SER* 3.2 3.4 + - - +
33D THR 2.7 5.5 + - - -
34D ARG* 1.3 77.4 - - + +
36D LYS* 1.3 68.6 + - - +
37D VAL 3.1 2.0 - - - -
38D LEU* 2.8 38.5 + - + +
39D GLU* 2.7 45.4 + - + +
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Residues in contact with LYS 36 (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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11D GLU 4.4 4.7 - - - -
12D ALA* 2.7 36.9 + - + +
13D SER* 3.4 15.8 + - - -
14D VAL* 5.8 2.5 - - + -
32D SER* 2.9 17.1 + - - +
33D THR* 3.0 6.7 + - - +
35D LYS* 1.3 75.1 - - - +
37D VAL* 1.3 58.4 + - - +
39D GLU* 3.6 5.8 - - - +
40D THR* 2.8 29.9 + - - +
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Residues in contact with VAL 37 (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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8D VAL* 3.6 26.7 - - + -
12D ALA* 3.6 15.3 - - + -
14D VAL* 4.6 7.6 - - + -
19D VAL* 4.0 17.0 - - + -
22D VAL* 3.3 33.4 - - + -
33D THR* 3.2 22.7 - - + +
36D LYS* 1.3 75.2 - - + +
38D LEU* 1.3 65.0 + - - +
39D GLU 2.9 5.2 - - - -
40D THR* 2.9 16.1 + - - -
41D ILE* 2.9 18.5 + - + +
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Residues in contact with LEU 38 (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* 4.2 13.2 - - + +
34D ARG* 2.7 32.3 + - + +
35D LYS* 2.8 35.6 + - - +
37D VAL* 1.3 82.0 - - - +
39D GLU* 1.3 75.3 + - - +
41D ILE* 3.9 15.6 - - - +
42D GLU* 4.2 7.5 + - - +
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Residues in contact with GLU 39 (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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35D LYS* 2.7 33.5 + - + +
36D LYS* 3.6 6.5 - - - +
38D LEU* 1.3 97.2 - - - +
40D THR* 1.3 52.7 + - - +
41D ILE 2.5 16.4 + - - -
42D GLU* 2.6 34.3 + - + +
43D ARG* 3.5 9.8 + - - +
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Residues in contact with THR 40 (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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8D VAL* 3.5 28.0 - - + +
11D GLU* 3.5 35.3 + - + +
12D ALA* 3.4 17.8 - - - +
36D LYS* 2.8 23.5 + - - +
37D VAL* 3.3 13.2 - - - -
39D GLU* 1.3 73.9 - - - +
41D ILE* 1.3 58.7 + - - +
42D GLU 3.6 0.2 - - - -
43D ARG* 4.3 5.9 - - - +
44D LEU* 3.4 22.3 + - + +
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Residues in contact with ILE 41 (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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8D VAL* 3.7 23.3 - - + -
19D VAL* 4.8 2.5 - - + -
22D VAL* 5.6 3.4 - - + -
23D VAL* 4.5 13.9 - - + -
37D VAL* 2.9 25.0 + - + +
38D LEU* 3.9 10.8 - - - +
39D GLU 2.5 6.1 + - - -
40D THR* 1.3 74.6 - - - +
42D GLU* 1.3 56.0 + - - +
44D LEU* 5.1 0.2 - - - -
45D GLY* 2.5 36.8 + - - +
46D TYR* 3.1 59.0 - - + +
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Residues in contact with GLU 42 (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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38D LEU* 4.2 6.3 + - - +
39D GLU* 2.6 31.8 + - + +
41D ILE* 1.3 76.0 - - - +
43D ARG* 1.3 64.3 + - + +
45D GLY* 3.5 6.7 + - - -
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Residues in contact with ARG 43 (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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39D GLU 3.5 8.7 + - - +
40D THR* 4.4 6.5 - - - +
41D ILE 3.3 0.2 - - - -
42D GLU* 1.3 77.0 - - + +
44D LEU* 1.3 64.6 + - - +
45D GLY* 3.0 5.1 + - - -
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Residues in contact with LEU 44 (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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1D MET* 4.5 9.9 - - + +
3D VAL* 3.6 31.4 - - + +
7D ASP* 4.4 16.6 - - + -
8D VAL* 4.7 7.9 - - + +
11D GLU* 3.4 33.9 - - + +
40D THR 3.4 16.6 + - - +
41D ILE 4.6 0.4 - - - +
43D ARG* 1.3 79.4 - - - +
45D GLY* 1.3 68.1 + - - +
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Residues in contact with GLY 45 (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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1D MET* 2.9 24.0 - - - +
3D VAL* 3.2 6.2 - - - +
41D ILE 2.5 18.1 + - - -
42D GLU* 3.9 7.2 - - - -
43D ARG 3.0 4.0 - - - -
44D LEU* 1.3 81.1 - - - +
46D TYR* 1.3 60.9 + - - -
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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