Contacts of the strand formed by residues 49 - 55 (chain E) in PDB entry 5MNJ
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 VAL 49 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36E THR* 4.3 17.3 - - + -
37E ILE 3.6 5.4 - - - +
38E MET* 4.9 14.1 - - + -
47E GLY 4.6 5.2 - - - +
48E GLY* 1.3 75.9 - - - +
50E PHE* 1.3 62.7 + - - +
51E PHE* 3.9 28.6 + - + -
71E THR* 4.1 3.3 + - - -
146E ALA* 2.9 26.5 + - - +
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Residues in contact with PHE 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E THR* 3.1 5.4 - - - -
37E ILE* 2.8 50.6 + - + +
39E GLY* 4.1 6.3 - - - -
45E TYR* 4.0 28.9 - + + -
48E GLY* 3.9 15.7 - - - -
49E VAL* 1.3 74.7 - - - +
51E PHE* 1.3 62.8 + - - +
52E LEU* 3.5 2.9 - - - +
69E PHE* 3.6 24.2 - + + -
71E THR* 3.6 20.6 - - + -
72E ARG 4.1 3.1 - - - -
73E ILE* 3.5 41.1 - - + -
110E LEU* 5.0 5.4 - - + -
142E THR* 4.1 11.0 - - + -
146E ALA* 3.4 25.4 - - + -
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Residues in contact with PHE 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E GLN* 4.0 29.4 - - + +
35E ALA 3.3 5.4 - - - -
36E THR* 3.3 27.6 - - + -
49E VAL* 3.9 25.6 - - + -
50E PHE* 1.3 76.4 - - - +
52E LEU* 1.3 65.8 - - - +
69E PHE* 3.5 4.7 - - - -
70E THR* 2.9 38.8 + - + +
71E THR* 2.7 22.7 + - - +
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Residues in contact with LEU 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E GLN* 3.4 9.5 - - - +
35E ALA* 2.8 41.4 + - + +
37E ILE* 3.4 34.5 - - + -
50E PHE 3.5 19.1 - - - +
51E PHE* 1.3 78.0 - - - +
53E THR* 1.3 66.1 + - - +
54E ILE* 5.2 0.4 - - + -
67E VAL* 3.8 25.1 - - + -
68E ALA 3.0 9.9 - - - +
69E PHE* 3.9 34.1 - - + -
70E THR* 3.9 4.4 - - - +
84E ILE* 4.2 3.1 - - + -
103E LEU* 4.2 8.3 - - + -
106E ILE* 4.3 4.3 - - + -
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Residues in contact with THR 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E VAL* 6.3 1.8 - - + -
33E TRP 3.5 7.2 - - - +
34E GLN* 5.8 3.8 - - + +
52E LEU* 1.3 73.9 - - - +
54E ILE* 1.3 64.6 + - - +
66E LYS 3.6 1.1 + - - +
67E VAL* 3.5 5.5 - - - +
68E ALA* 2.7 46.4 + - - +
70E THR* 3.5 23.7 - - + +
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Residues in contact with ILE 54 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E PHE 3.6 0.7 - - - +
32E HIS* 3.3 6.0 - - - +
33E TRP* 2.7 60.7 + - + +
35E ALA* 3.9 25.8 - - + -
52E LEU 5.1 0.4 - - - -
53E THR* 1.3 82.6 - - - +
55E HIS* 1.3 62.0 + - - +
56E PHE* 4.0 14.0 + - + -
65E PRO* 3.9 16.8 - - + -
66E LYS 3.4 3.8 - - - +
67E VAL* 4.2 14.4 - - + -
99E ILE* 3.7 48.9 - - + -
103E LEU* 4.7 4.5 - - + -
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Residues in contact with HIS 55 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E PHE* 3.3 11.4 - - + +
32E HIS* 2.8 46.6 + + + -
53E THR 4.3 0.2 - - - -
54E ILE* 1.3 73.7 - - - +
56E PHE* 1.3 75.2 + - - +
57E PRO* 3.8 5.9 - - + +
65E PRO* 3.5 1.1 - - - +
66E LYS* 2.7 57.6 + - + +
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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