Contacts of the helix formed by residues 41 - 54 (chain B) in PDB entry 5XOU
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 GLU 41 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B PRO* 2.9 17.7 - - - +
38B GLY* 2.6 36.5 + - - +
40B GLU* 1.3 79.3 - - + +
42B VAL* 1.3 59.3 + - - +
43B TYR 3.5 2.5 - - - -
44B PRO* 2.9 29.1 - - + +
45B LEU* 3.4 12.3 + - - +
81B ARG* 5.5 5.5 - - - +
82B MET* 6.2 0.2 - - - +
86B TYR* 3.2 22.1 + - - -
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Residues in contact with VAL 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU* 5.5 0.9 - - + -
37B PRO* 3.7 24.9 - - + +
38B GLY 3.2 21.6 + - - +
39B ARG* 3.8 16.4 - - - +
41B GLU* 1.3 74.6 - - - +
43B TYR* 1.3 67.9 + - + +
45B LEU* 2.8 7.0 + - - +
46B LEU* 2.8 56.3 + - + -
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Residues in contact with TYR 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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39B ARG 5.6 4.5 + - - -
40B GLU 5.2 3.5 + - - -
41B GLU 5.0 0.2 - - - +
42B VAL* 1.3 81.7 - - + +
44B PRO* 1.3 72.8 - - + +
46B LEU* 3.3 7.6 + - + +
47B ALA* 3.1 21.0 + - - +
59B ARG* 3.6 42.6 + - - +
61B GLY 4.5 7.9 - - - -
62B ASP* 5.9 1.6 - - - -
4F A 3.7 22.1 - + + +
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Residues in contact with PRO 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B GLU 4.5 5.4 - - - +
41B GLU* 2.9 32.8 - - + +
43B TYR* 1.3 87.4 - - + +
45B LEU* 1.3 54.9 + - + +
47B ALA 3.2 1.0 + - - -
48B GLN* 2.9 26.2 + - - +
4F A 3.0 66.9 + - + +
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Residues in contact with LEU 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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33B LEU* 4.1 16.2 - - + -
37B PRO* 3.5 28.3 - - + -
41B GLU* 3.4 13.0 + - - +
42B VAL* 2.8 9.3 + - - +
44B PRO* 1.3 78.0 - - + +
46B LEU* 1.3 61.7 + - - +
48B GLN* 3.1 15.3 + - + +
49B VAL* 2.9 33.1 + - - +
79B LEU* 5.2 9.0 - - + -
81B ARG* 3.9 24.7 - - + -
86B TYR* 3.2 42.4 - - + -
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Residues in contact with LEU 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B VAL* 4.1 22.4 - - + -
33B LEU* 3.8 26.5 - - + -
42B VAL* 2.8 35.6 + - + +
43B TYR* 3.7 8.1 - - + +
45B LEU* 1.3 74.6 - - - +
47B ALA* 1.3 58.6 + - - +
49B VAL* 3.1 6.6 + - + +
50B ALA* 2.8 28.6 + - - +
59B ARG* 3.9 26.7 - - + -
62B ASP* 3.2 36.1 - - + +
63B GLY* 4.5 2.0 - - - +
64B LEU* 4.1 7.2 - - + +
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Residues in contact with ALA 47 (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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43B TYR 3.1 11.1 + - - +
44B PRO 3.4 9.0 - - - +
46B LEU* 1.3 77.4 - - - +
48B GLN* 1.3 62.3 + - - +
50B ALA* 3.1 11.9 + - - +
51B ARG* 3.0 22.3 + - - +
59B ARG* 4.8 10.0 - - + +
115B ARG* 4.6 4.3 + - - +
4F A 3.7 34.5 - - - +
5F C 4.2 11.1 + - - +
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Residues in contact with GLN 48 (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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44B PRO 2.9 12.9 + - - +
45B LEU* 3.1 19.1 + - - +
47B ALA* 1.3 75.1 - - - +
49B VAL* 1.3 62.7 + - - +
51B ARG* 3.0 45.7 + - - +
52B ARG* 3.0 19.5 + - + +
79B LEU* 3.5 36.2 - - + +
80B ALA 3.8 21.5 + - - +
81B ARG* 4.8 3.6 - - - +
4F A 4.6 13.2 + - - +
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Residues in contact with VAL 49 (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 VAL* 4.3 9.0 - - + -
33B LEU* 4.0 17.5 - - + -
45B LEU 2.9 19.0 + - - +
46B LEU* 3.1 11.4 + - - +
48B GLN* 1.3 74.8 - - - +
50B ALA* 1.3 64.3 + - - +
52B ARG* 3.1 3.0 + - - +
53B ALA* 2.9 23.6 + - - +
64B LEU* 3.9 9.9 - - + -
79B LEU* 3.3 31.0 - - + -
88B TYR* 4.2 13.8 - - + -
90B LEU* 3.7 31.2 - - + -
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Residues in contact with ALA 50 (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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46B LEU 2.8 11.8 + - - +
47B ALA* 3.2 14.8 - - - +
49B VAL* 1.3 77.9 - - - +
51B ARG* 1.3 63.1 + - - +
53B ALA* 3.6 8.0 + - - +
54B GLY 3.7 6.4 + - - +
55B GLY 5.4 0.3 - - - +
57B THR* 3.6 18.4 - - - +
58B VAL* 4.1 15.7 - - - -
59B ARG 4.3 0.7 - - - +
64B LEU* 4.2 14.8 - - + +
115B ARG* 3.6 25.8 + - - +
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Residues in contact with ARG 51 (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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47B ALA 3.0 8.9 + - - +
48B GLN* 3.0 41.8 + - - +
50B ALA* 1.3 75.6 - - - +
52B ARG* 1.3 67.1 + - - +
54B GLY* 2.9 22.0 + - - -
115B ARG* 3.5 19.0 - - - +
4F A 4.4 8.9 + - - -
5F C 4.0 31.6 + - - +
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Residues in contact with ARG 52 (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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48B GLN* 3.0 20.1 + - + +
49B VAL 3.1 4.2 + - - +
51B ARG* 1.3 83.5 - - + +
53B ALA* 1.3 58.3 + - - +
54B GLY* 3.3 0.9 + - - -
74B VAL* 2.7 22.8 - - - +
78B THR* 3.4 21.2 + - - +
79B LEU* 3.4 26.2 - - + +
88B TYR* 3.9 18.8 - - + +
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Residues in contact with ALA 53 (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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49B VAL 2.9 16.1 + - - +
50B ALA* 3.8 8.3 - - - +
51B ARG 3.0 0.2 - - - -
52B ARG* 1.3 79.3 - - - +
54B GLY* 1.3 62.4 + - - +
57B THR* 4.7 3.6 - - - +
64B LEU* 4.9 0.4 - - + -
72B VAL 4.6 1.2 - - - +
73B LEU* 3.4 21.5 - - + +
74B VAL* 2.8 37.7 + - - +
88B TYR* 4.2 1.3 + - + -
90B LEU* 3.7 28.3 - - + -
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Residues in contact with GLY 54 (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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50B ALA 3.7 1.8 + - - +
51B ARG 2.9 17.0 + - - -
52B ARG 3.2 1.5 - - - -
53B ALA* 1.3 82.0 - - - +
55B GLY* 1.3 70.6 + - - +
57B THR* 3.0 19.1 + - - -
72B VAL 5.6 0.2 - - - -
73B LEU* 3.1 7.2 - - - +
74B VAL* 4.9 1.1 - - - -
119B GLU* 5.9 0.7 - - - -
122B ARG* 6.0 2.0 - - - -
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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