Contacts of the helix formed by residues 31 - 40 (chain B) in PDB entry 2PG4
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 31 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29B GLU 4.0 1.2 + - - -
30B PRO* 1.3 76.7 - - - +
32B LEU* 1.3 65.6 + - - +
33B ALA* 3.7 8.4 + - - +
34B GLU* 3.0 31.6 + - - +
35B ILE* 3.2 20.0 + - - +
65B LEU* 5.1 1.0 - - - +
69B VAL* 3.8 33.7 - - - -
70B LYS 3.1 8.7 - - - -
100B PEG 4.1 2.5 - - - -
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Residues in contact with LEU 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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31B SER* 1.3 74.9 - - - +
33B ALA* 1.3 57.1 + - - +
35B ILE* 3.1 9.7 + - + +
36B VAL* 3.0 31.7 + - - +
46B PHE* 3.9 14.2 - - + -
47B PHE* 4.0 30.5 - - + -
51B LYS* 4.5 1.3 - - + -
62B GLU* 3.7 21.1 - - - +
70B LYS* 3.1 20.8 + - + +
71B THR* 3.8 26.7 - - - +
72B LEU* 3.8 23.1 - - + -
100B PEG 3.5 29.4 + - - +
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Residues in contact with ALA 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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31B SER* 3.7 8.0 + - - +
32B LEU* 1.3 75.0 - - - +
34B GLU* 1.3 60.2 + - + +
36B VAL* 3.5 8.7 + - - +
37B LYS* 3.0 29.6 + - - +
47B PHE* 5.5 2.6 - - - -
100B PEG 4.8 1.8 + - - +
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Residues in contact with GLU 34 (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 PHE* 4.3 8.2 - - + -
28B TYR* 2.6 33.7 + - - -
29B GLU 4.4 1.0 - - - +
30B PRO* 3.2 15.5 - - + +
31B SER* 3.0 40.0 + - - +
33B ALA* 1.3 77.8 - - + +
35B ILE* 1.3 57.3 + - - +
37B LYS* 4.2 4.2 - - - +
38B ALA* 2.9 33.4 + - - +
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Residues in contact with ILE 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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16B ILE* 4.1 26.0 - - + -
19B THR* 4.3 6.6 - - + +
20B LEU* 3.8 32.3 - - + -
23B PHE* 4.7 6.3 - - + -
30B PRO* 3.8 18.4 - - + +
31B SER 3.2 16.3 + - - +
32B LEU* 3.1 21.0 + - + +
34B GLU* 1.3 77.4 - - - +
36B VAL* 1.3 55.1 + - - +
39B SER* 2.6 37.7 + - - +
46B PHE* 4.3 10.5 - - + -
72B LEU* 3.8 30.1 - - + +
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Residues in contact with VAL 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 LEU 3.0 15.1 + - - +
33B ALA* 3.6 10.5 - - - +
35B ILE* 1.3 74.8 - - - +
37B LYS* 1.3 63.2 + - + +
39B SER* 3.2 6.7 + - - -
40B GLY* 3.1 19.1 + - - -
41B VAL* 3.3 30.5 - - + +
42B SER* 3.9 0.7 - - - -
43B GLU* 3.7 24.9 - - + +
46B PHE* 3.7 37.7 - - + -
47B PHE* 4.6 8.1 - - + -
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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 ALA 3.0 17.8 + - - +
34B GLU* 4.2 4.0 - - - +
36B VAL* 1.3 81.0 - - + +
38B ALA* 1.3 65.8 + - - +
39B SER 3.2 0.2 + - - -
40B GLY* 3.3 9.6 + - - -
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Residues in contact with ALA 38 (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 THR* 3.9 22.2 + - + -
23B PHE* 3.9 15.0 - - + -
34B GLU 2.9 18.8 + - - +
37B LYS* 1.3 79.4 - - - +
39B SER* 1.3 61.1 + - - +
40B GLY* 3.6 0.3 + - - -
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Residues in contact with SER 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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15B ARG* 3.0 54.6 + - - +
16B ILE* 3.6 11.7 - - - +
19B THR* 3.6 13.0 + - - -
35B ILE 2.6 25.6 + - - -
36B VAL 3.2 6.9 + - - -
38B ALA* 1.3 79.0 - - - +
40B GLY* 1.3 55.5 + - - +
41B VAL* 3.3 18.9 - - - +
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Residues in contact with GLY 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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15B ARG* 3.6 17.1 + - - -
36B VAL 3.1 8.4 + - - -
37B LYS 3.3 9.2 + - - -
38B ALA 3.4 0.4 + - - -
39B SER* 1.3 76.8 - - - +
41B VAL* 1.3 61.2 + - - +
42B SER 4.1 0.3 + - - -
97B CIT 4.0 11.6 + - - +
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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