Contacts of the helix formed by residues 34 - 45 (chain B) in PDB entry 2P1N
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 34 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139A ILE* 3.8 24.0 - - + -
140A LYS 4.1 4.0 - - - +
142A ASP* 3.1 17.3 - - - +
143A PHE* 3.7 10.7 - - - -
31B SER 4.5 0.2 - - - +
32B LEU 3.5 2.0 - - - -
33B VAL* 1.3 80.2 - - - +
35B LYS* 1.3 67.4 + - - +
36B SER* 3.4 14.1 - - - -
37B TRP* 2.9 50.0 + - - +
38B TYR* 3.3 9.5 + - - +
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Residues in contact with LYS 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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142A ASP* 2.8 34.4 + - - +
143A PHE* 3.6 34.1 - - + -
147A GLU* 4.7 15.0 + - - +
34B CYS* 1.3 68.9 - - - +
36B SER* 1.3 61.5 + - - +
38B TYR* 3.4 23.1 - - - +
39B GLU* 3.0 49.1 + - + +
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Residues in contact with SER 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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142A ASP* 4.7 1.6 + - - -
11B GLU* 5.8 1.6 - - - +
14B LEU* 4.9 3.1 - - - +
34B CYS* 2.9 15.1 + - - -
35B LYS* 1.3 76.1 - - - +
37B TRP* 1.3 65.0 + - - +
39B GLU* 3.3 7.5 + - - +
40B ILE* 3.1 39.4 + - - +
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Residues in contact with TRP 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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125A ILE* 4.5 13.7 - - + -
133A ILE* 3.8 18.4 - - + -
137A PHE* 4.1 22.7 - + - -
139A ILE* 3.9 27.7 - - + +
9B PHE* 5.9 0.2 - + - -
14B LEU* 3.5 36.4 - - + +
17B VAL* 6.3 1.1 - - + -
18B PHE* 3.7 29.1 - + + -
30B VAL* 3.3 26.2 - - + +
33B VAL* 3.4 29.8 - - + -
34B CYS* 2.9 23.7 + - - +
36B SER* 1.3 80.1 - - - +
38B TYR* 1.3 67.7 + - - +
40B ILE* 3.1 6.3 + - - +
41B GLU* 3.0 27.0 + - - +
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Residues in contact with TYR 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A PHE* 4.0 15.7 - + + -
151A VAL* 3.7 28.5 - - + +
154A GLU* 5.1 0.7 + - - -
31B SER* 3.3 29.4 + - - +
34B CYS 3.3 3.0 + - - -
35B LYS* 3.4 22.0 - - - +
37B TRP* 1.3 79.6 - - - +
39B GLU* 1.3 78.0 + - + +
41B GLU* 4.2 1.2 - - - +
42B ARG* 3.0 50.0 + - - +
64B ARG* 3.4 51.2 + - - +
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Residues in contact with GLU 39 (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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35B LYS* 3.0 31.2 + - + +
36B SER* 3.8 7.9 - - - +
37B TRP 3.2 0.2 - - - -
38B TYR* 1.3 85.8 - - + +
40B ILE* 1.3 68.8 + - + +
42B ARG* 2.6 46.7 + - - +
43B TRP* 3.0 31.9 + - + -
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Residues in contact with ILE 40 (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 GLU* 3.3 44.6 - - + +
12B GLU 5.2 1.6 - - - +
14B LEU* 3.6 22.0 - - + -
15B GLU* 3.8 35.4 - - + +
18B PHE* 3.6 18.2 - - + -
36B SER* 3.1 23.2 + - - +
37B TRP 3.1 0.8 + - - +
39B GLU* 1.3 80.6 - - + +
41B GLU* 1.3 59.4 + - - +
43B TRP* 3.5 4.7 + - - +
44B CYS* 3.1 27.4 + - - -
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Residues in contact with GLU 41 (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 PHE* 3.8 16.2 - - + -
27B ARG* 3.3 35.3 + - - +
30B VAL* 3.8 10.8 - - + -
31B SER* 3.6 27.6 - - - -
37B TRP 3.0 12.4 + - - +
38B TYR 4.4 0.9 - - - +
40B ILE* 1.3 75.0 - - - +
42B ARG* 1.3 78.6 + - - +
43B TRP 2.8 2.4 + - - -
44B CYS* 3.0 2.0 + - - -
45B ARG* 2.9 64.3 + - - +
64B ARG* 4.0 2.1 + - - -
65B PHE* 3.3 10.0 - - - -
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Residues in contact with ARG 42 (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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38B TYR* 3.0 42.8 + - + +
39B GLU* 2.6 54.1 + - - +
41B GLU* 1.3 82.8 + - - +
43B TRP* 1.3 93.6 + - + +
45B ARG 3.7 3.5 + - - -
63B ARG* 3.2 24.7 + - - +
64B ARG* 3.2 27.3 + - - +
65B PHE* 3.5 32.6 - - - +
66B PRO* 3.6 4.5 - - - +
67B LYS 4.9 0.9 + - - -
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Residues in contact with TRP 43 (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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15B GLU* 5.9 1.1 - - - +
39B GLU* 3.0 28.7 + - + +
40B ILE* 3.5 5.9 + - - +
41B GLU 2.8 4.2 + - - -
42B ARG* 1.3 115.6 - - + +
44B CYS* 1.3 59.9 + - - +
45B ARG 3.7 0.2 - - - -
66B PRO* 3.7 29.2 - - + -
67B LYS* 3.3 53.1 - - + +
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Residues in contact with CYS 44 (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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15B GLU* 4.1 34.8 - - + +
18B PHE* 3.9 22.4 - - - -
19B SER* 5.3 1.1 - - - -
27B ARG* 3.3 33.0 + - - +
40B ILE 3.1 22.7 - - - +
41B GLU 3.0 3.0 + - - -
43B TRP* 1.3 82.2 - - + +
45B ARG* 1.3 60.7 + - - +
46B ARG* 3.4 13.7 + - - +
67B LYS* 5.1 2.7 - - - +
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Residues in contact with ARG 45 (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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159A PHE* 4.0 18.0 + - - +
24B ASP* 4.7 6.1 + - - +
27B ARG* 3.5 35.1 + - + +
28B ASN* 2.9 29.6 + - - +
41B GLU* 2.9 53.1 + - - +
42B ARG 3.7 1.5 + - - +
43B TRP 3.7 2.2 - - - -
44B CYS* 1.3 69.0 - - - +
46B ARG* 1.3 62.0 + - - +
47B LYS 3.4 24.1 + - - +
48B VAL* 4.2 5.5 - - - +
64B ARG* 4.6 4.2 - - - +
65B PHE* 3.2 49.6 - - + +
67B LYS* 3.9 4.5 + - - +
68B VAL* 3.5 23.6 + - - +
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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