Contacts of the strand formed by residues 47 - 53 (chain A) in PDB entry 1MRJ
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 TYR 47 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A GLY 3.6 14.7 + - - -
44A SER 5.4 0.5 - - - +
45A GLN 3.4 4.1 - - - +
46A ARG* 1.3 133.8 + - + +
48A ALA* 1.3 62.3 + - - +
49A LEU* 5.7 2.4 - - - +
63A ALA* 5.2 1.6 - - + -
64A ILE 3.2 17.7 - - - +
65A ASP* 4.0 11.1 + - + -
66A VAL* 4.2 2.7 - - - -
72A MET* 4.1 14.8 - - + -
87A SER 4.2 2.1 + - - -
90A GLU* 3.5 13.3 - - - +
91A ALA* 3.5 25.7 + - + +
94A TYR* 3.8 25.8 - + + -
95A VAL* 3.7 24.0 - - + -
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Residues in contact with ALA 48 (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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1A ASP* 6.1 1.6 - - - -
2A VAL* 6.5 0.4 - - + -
21A LEU* 6.0 0.4 - - + -
24A ALA* 5.0 15.3 - - + +
47A TYR* 1.3 75.2 - - - +
49A LEU* 1.3 65.8 + - - +
50A ILE* 5.7 1.1 - - + -
62A VAL 3.5 1.7 - - - +
63A ALA* 3.5 2.6 - - - -
64A ILE* 2.9 48.1 + - + +
66A VAL* 3.7 19.0 - - + +
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Residues in contact with LEU 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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1A ASP* 3.4 28.1 + - - +
2A VAL* 3.2 21.3 + - - +
47A TYR 5.7 2.0 - - - +
48A ALA* 1.3 82.9 - - - +
50A ILE* 1.3 62.6 + - - +
51A HIS* 4.0 20.9 - - + -
61A SER* 5.3 0.4 - - - -
62A VAL 3.3 2.7 - - - +
63A ALA* 4.0 16.8 - - + -
95A VAL* 4.4 16.6 - - + -
96A PHE* 3.8 30.1 - - + +
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Residues in contact with ILE 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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2A VAL* 3.1 16.8 - - + +
17A PHE* 3.3 34.1 - - + -
21A LEU* 4.5 17.7 - - + -
48A ALA* 5.1 1.3 - - + -
49A LEU* 1.3 77.0 - - - +
51A HIS* 1.3 62.4 + - - +
52A LEU* 3.8 21.4 + - + -
60A ILE 3.9 0.5 - - - +
61A SER* 3.3 2.8 - - - -
62A VAL* 2.8 44.4 + - + +
64A ILE* 4.4 22.4 - - + -
158A THR* 3.7 23.6 - - + -
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Residues in contact with HIS 51 (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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1A ASP* 2.7 37.9 + - + +
2A VAL 2.8 18.3 + - - -
3A SER* 3.3 18.6 - - - +
4A PHE 2.9 27.0 + - - +
5A ARG* 5.8 3.4 - - - +
49A LEU* 4.0 18.5 - - + +
50A ILE* 1.3 73.3 - - - +
52A LEU* 1.3 62.0 + - - +
53A THR* 5.1 1.6 - - - +
59A THR* 4.4 11.1 - - + +
60A ILE 3.5 5.8 - - - +
61A SER* 2.7 28.5 + - - +
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Residues in contact with LEU 52 (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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4A PHE* 3.4 36.8 - - + +
17A PHE* 3.9 6.1 - - + -
50A ILE* 3.8 31.9 - - + +
51A HIS* 1.3 77.7 - - - +
53A THR* 1.3 61.0 + - - +
58A GLU 3.8 0.9 - - - +
59A THR* 3.2 3.8 - - - +
60A ILE* 2.9 39.0 + - + +
62A VAL* 4.5 6.7 - - + -
132A LEU* 4.6 13.5 - - + -
136A ILE* 3.8 20.1 - - + +
154A LEU* 3.5 32.5 - - + -
158A THR* 4.3 5.2 - - + -
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Residues in contact with THR 53 (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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4A PHE 3.0 7.6 + - - -
5A ARG* 3.6 37.9 + - + +
6A LEU* 2.8 31.7 + - - +
51A HIS* 5.1 1.4 - - - +
52A LEU* 1.3 73.4 + - - +
54A ASN* 1.3 63.5 + - - +
57A ASP* 3.4 41.5 - - - +
58A GLU 3.3 3.1 - - - -
59A THR* 2.8 27.4 + - - +
136A ILE* 4.3 2.2 - - - +
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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