Contacts of the helix formed by residues 31 - 42 (chain B) in PDB entry 5C5A
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 31 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A ALA* 5.4 0.4 - - - +
45A LYS* 4.6 4.2 - - - +
52A GLU* 2.7 41.0 + - - +
55A PHE* 3.3 25.1 - - + -
56A TYR* 2.9 33.4 + - + +
29B ARG 3.7 0.4 + - - -
30B PRO* 1.3 72.8 - - - +
32B PRO* 1.4 77.0 - - + +
33B LEU 3.3 0.7 - - - +
34B LEU 3.0 5.9 + - - +
35B LEU* 2.9 19.2 + - - +
105B ARG 3.0 13.8 + - - +
106B ASN* 3.0 45.6 + - + +
107B LEU 3.7 1.8 - - - +
206B IOD 4.0 13.0 - - + -
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Residues in contact with PRO 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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51A LYS* 4.0 33.2 - - + +
55A PHE* 3.7 31.9 - - + -
30B PRO 3.8 0.4 - - - +
31B LYS* 1.4 86.8 - - + +
33B LEU* 1.3 58.5 + - - +
35B LEU* 3.3 12.5 + - + +
36B LYS* 2.9 26.0 + - - +
206B IOD 3.9 9.2 - - + -
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Residues in contact with LEU 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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25A GLU* 5.7 4.5 - - - +
49A THR* 6.0 4.7 - - + +
51A LYS* 4.3 25.1 - - + +
31B LYS 3.3 0.8 - - - -
32B PRO* 1.3 75.0 - - - +
34B LEU* 1.3 66.4 + - - +
36B LYS* 3.3 27.9 + - + +
37B LEU* 3.1 20.3 + - - +
81B LEU* 3.9 22.3 - - + +
84B ASP* 6.0 3.8 - - + -
85B LEU* 3.6 20.3 - - + +
206B IOD 3.7 22.2 - - + +
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Residues in contact with LEU 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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30B PRO* 3.8 17.5 - - + -
31B LYS* 3.0 9.7 + - + +
33B LEU* 1.3 75.8 - - - +
35B LEU* 1.3 59.5 + - - +
37B LEU* 3.1 4.2 + - + +
38B LEU* 2.9 42.4 + - + +
53B VAL* 4.5 10.5 - - + -
57B LEU* 4.2 27.1 - - + -
85B LEU* 3.7 19.7 - - + +
86B PHE* 6.3 1.3 - - + -
103B ILE* 4.8 3.4 - - + +
106B ASN* 3.4 42.6 - - + +
107B LEU* 4.4 14.4 - - + -
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Residues in contact with LEU 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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30B PRO* 3.9 16.5 - - + +
31B LYS 2.9 13.1 + - - +
32B PRO* 3.4 13.2 - - + +
34B LEU* 1.3 76.9 - - - +
36B LYS* 1.3 55.8 + - - +
38B LEU* 3.2 2.2 + - - -
39B LYS* 2.8 45.4 + - + +
44B GLN* 4.2 19.7 - - + +
45B LYS 4.0 11.0 - - - +
48B TYR* 3.5 37.0 - - + +
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Residues in contact with LYS 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 PRO 2.9 14.2 + - - +
33B LEU* 3.4 29.2 - - + +
34B LEU 3.2 0.2 - - - -
35B LEU* 1.3 76.4 - - - +
37B LEU* 1.3 62.9 + - - +
39B LYS* 3.4 9.7 + - - +
40B SER* 3.3 20.1 + - - -
81B LEU* 4.3 15.3 - - + -
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Residues in contact with LEU 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 LEU 3.1 9.3 + - - +
34B LEU* 3.1 8.9 + - + +
36B LYS* 1.3 75.9 - - - +
38B LEU* 1.3 75.2 + - + +
40B SER* 2.8 26.0 + - - -
41B VAL* 3.6 5.4 + - + +
57B LEU* 3.7 31.0 - - + -
60B TYR* 3.7 52.3 - - + +
81B LEU* 3.8 16.3 - - + +
82B LEU* 4.2 12.3 - - + +
85B LEU* 3.8 23.1 - - + -
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Residues in contact with LEU 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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30B PRO* 4.1 10.8 - - + -
34B LEU* 2.9 40.9 + - + +
35B LEU* 3.7 4.3 - - - +
37B LEU* 1.3 83.3 - - + +
39B LYS* 1.3 58.1 + - - +
41B VAL* 3.2 6.0 + - - +
42B GLY* 2.7 32.8 + - - -
43B ALA 4.9 0.9 - - - -
48B TYR* 4.0 40.4 - - + +
53B VAL* 4.3 24.0 - - + +
56B TYR* 3.7 34.2 - - + -
57B LEU* 4.8 1.1 - - + +
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Residues in contact with LYS 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 LEU* 2.8 39.1 + - + +
36B LYS* 3.8 7.0 - - - +
37B LEU 3.2 0.2 - - - -
38B LEU* 1.3 76.3 - - - +
40B SER* 1.3 61.0 + - - +
42B GLY 3.3 17.1 - - - +
43B ALA 4.9 0.2 - - - -
44B GLN* 3.2 58.3 + - + +
48B TYR* 4.7 0.2 - - - +
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Residues in contact with SER 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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36B LYS 3.3 11.0 + - - -
37B LEU* 2.8 20.4 + - - -
39B LYS* 1.3 77.5 - - - +
41B VAL* 1.3 58.5 + - - +
60B TYR* 3.6 23.6 - - - -
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Residues in contact with VAL 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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37B LEU* 3.8 9.6 - - + +
38B LEU* 3.3 11.0 - - - +
39B LYS 4.6 0.2 - - - -
40B SER* 1.3 85.3 + - - +
42B GLY* 1.3 59.8 + - - +
56B TYR* 3.8 37.4 - - + +
59B GLN* 4.0 17.9 - - + +
60B TYR* 3.9 30.3 - - + +
63B THR* 4.5 10.1 - - + +
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Residues in contact with GLY 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 LEU 2.7 16.2 + - - +
39B LYS* 3.3 15.9 - - - +
41B VAL* 1.3 75.5 - - - +
43B ALA* 1.3 64.4 + - - -
44B GLN 4.0 0.5 + - - -
56B TYR* 3.4 23.3 - - - -
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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