Contacts of the strand formed by residues 47 - 52 (chain A) in PDB entry 1MVL
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 47 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LYS* 4.1 17.7 - - + +
20A PRO 2.9 11.7 + - - +
21A ARG* 3.5 18.9 + - + +
22A VAL* 2.7 31.0 + - - +
46A ALA* 1.3 72.4 - - - +
48A VAL* 1.3 58.4 + - - +
49A ARG* 4.7 7.9 + - + -
68A GLU* 6.1 0.4 - - - -
96A TRP* 3.7 31.2 + - + -
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Residues in contact with VAL 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A VAL* 3.3 6.5 - - + +
24A LEU* 3.6 27.4 - - + -
39A CYS* 4.5 5.8 - - + +
42A PHE* 3.6 34.5 - - + +
43A THR* 3.9 7.0 - - + +
46A ALA* 3.6 14.1 + - + +
47A GLU* 1.3 80.4 - - - +
49A ARG* 1.3 77.9 + - - +
68A GLU* 4.8 3.3 + - - +
69A VAL* 3.9 39.8 - - + +
70A THR 4.4 1.0 + - - -
96A TRP* 5.1 0.2 - - - -
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Residues in contact with ARG 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A VAL 3.1 4.8 + - - -
23A LEU* 3.4 18.7 - - + +
24A LEU* 2.9 24.9 + - - -
47A GLU* 4.7 7.0 + - + +
48A VAL* 1.3 81.6 - - - +
50A ALA* 1.3 61.1 + - - +
69A VAL* 4.3 0.4 - - - -
70A THR* 3.8 10.9 - - - +
72A TYR* 3.5 33.9 + - + +
92A GLU* 5.3 1.2 + - - +
93A LEU* 3.7 18.0 - - - +
96A TRP* 3.5 61.8 - - + +
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Residues in contact with ALA 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LEU 3.2 3.6 - - - -
35A PHE* 3.6 30.1 - - + -
39A CYS* 4.4 4.0 - - - -
49A ARG* 1.3 74.4 - - - +
51A VAL* 1.3 58.5 + - - +
65A LEU* 4.8 1.3 - - + -
69A VAL* 3.9 17.7 - - + +
70A THR 3.0 8.6 + - - +
71A LEU* 3.8 14.6 - - + -
72A TYR* 2.8 38.0 + - - -
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Residues in contact with VAL 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 4.0 14.6 - - + -
24A LEU 2.9 6.8 + - - +
25A ALA* 3.1 14.6 - - + +
26A ALA 2.9 24.4 + - - +
35A PHE* 4.5 0.2 - - - -
50A ALA* 1.3 77.6 - - - +
52A VAL* 1.3 69.3 + - - +
72A TYR* 3.5 3.1 - - + -
93A LEU* 3.9 18.2 - - + -
100A LEU* 6.1 0.2 - - + -
121A LEU* 3.9 19.7 - - + -
122A LEU* 3.9 37.9 - - + +
125A ILE* 3.8 21.3 - - + -
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Residues in contact with VAL 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ALA* 3.5 17.0 - - + -
35A PHE* 4.4 9.2 - - + -
51A VAL* 1.3 83.9 - - - +
53A THR* 1.3 62.5 + - - +
56A SER* 3.1 16.6 - - - +
57A LEU* 3.8 26.0 - - + -
60A LEU* 5.1 7.4 - - + -
71A LEU* 3.4 27.1 - - + -
72A TYR 3.1 17.6 + - - +
73A THR* 3.9 24.3 - - + -
74A ASP* 4.4 7.4 + - - +
121A LEU* 5.3 0.7 - - - +
122A LEU* 5.3 1.3 + - - +
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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