Contacts of the strand formed by residues 49 - 54 (chain R) in PDB entry 4M8B
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 ASN 49 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5R PRO* 3.9 15.3 - - + +
7R CYS 4.2 2.5 - - - -
8R TYR* 3.9 20.5 - - - -
43R GLU 3.6 9.5 + - - -
44R LEU 2.9 31.5 + - - +
46R ASN* 3.1 29.6 + - - +
47R PRO 4.4 1.7 - - - +
48R GLY* 1.3 78.2 - - - +
50R ILE* 1.3 60.5 + - - +
51R PHE* 3.8 16.1 - - + -
141R ILE 3.9 0.5 - - - +
142R ALA* 3.5 1.9 - - - -
143R TYR* 2.9 30.1 + - + -
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Residues in contact with ILE 50 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5R PRO* 3.6 2.8 - - - +
6R THR* 2.7 33.9 + - - -
7R CYS* 3.1 38.7 + - - +
8R TYR 4.4 0.4 - - - -
9R GLY* 3.9 26.9 - - - +
11R ILE* 3.5 30.1 - - + -
20R VAL* 4.5 7.6 - - + -
48R GLY 3.9 5.8 - - - +
49R ASN* 1.3 80.3 - - - +
51R PHE* 1.3 62.8 + - - +
52R VAL* 4.7 0.7 - - + -
140R LEU* 4.3 21.8 - - + -
141R ILE 3.3 7.6 - - - +
142R ALA* 4.0 11.0 - - + -
157R PRO* 5.1 2.2 - - + -
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Residues in contact with PHE 51 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3R PRO 5.4 0.4 - - - -
4R GLY* 4.0 5.8 - - - -
5R PRO* 3.6 28.3 - - + -
6R THR* 3.9 2.7 - - - -
32R ILE* 3.7 27.1 - - + -
44R LEU* 3.4 54.1 - - + -
49R ASN* 3.8 18.4 - - + -
50R ILE* 1.3 74.5 - - - +
52R VAL* 1.3 66.3 + - - +
53R PHE* 5.1 1.3 - - + -
63R TRP* 3.9 22.0 - + + -
139R HIS 3.6 0.5 - - - +
140R LEU* 3.3 5.5 - - - +
141R ILE* 2.7 48.6 + - + +
143R TYR* 3.8 24.0 - + - -
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Residues in contact with VAL 52 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6R THR* 3.4 13.6 + - + -
20R VAL* 3.8 28.7 - - + -
21R PHE* 4.2 18.2 - - + -
24R VAL* 4.2 28.7 - - + -
31R CYS* 3.1 10.7 - - + -
32R ILE* 2.8 24.0 + - - +
50R ILE* 4.7 1.3 - - + -
51R PHE* 1.3 82.0 - - - +
53R PHE* 1.3 70.7 + - - +
138R PHE* 4.6 7.4 - - + -
139R HIS 3.1 9.4 - - - +
140R LEU* 4.0 16.4 - - + -
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Residues in contact with PHE 53 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31R CYS* 4.2 2.5 - - - -
32R ILE* 3.4 28.0 - - + +
51R PHE 5.1 0.7 - - - -
52R VAL* 1.3 83.4 - - - +
54R ASN* 1.3 61.4 + - - +
55R GLU 3.6 0.5 + - - -
58R SER* 3.8 7.9 - - - +
60R ILE* 3.4 50.5 - - + -
63R TRP* 3.4 43.1 - + + -
138R PHE* 3.6 2.6 - - - -
139R HIS* 2.9 70.4 + + + -
141R ILE* 4.2 9.0 - - + -
301R EDO 3.9 6.1 - - - -
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Residues in contact with ASN 54 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31R CYS* 4.7 12.5 - - - +
32R ILE 4.7 1.8 + - - -
53R PHE* 1.3 71.1 - - - +
55R GLU* 1.3 58.1 + - - +
56R GLU* 2.9 28.9 + - - +
57R LYS* 3.5 36.5 + - + +
58R SER* 2.5 34.4 + - - -
136R GLU* 2.8 30.1 + - - +
137R THR 3.6 6.0 - - - +
138R PHE* 3.7 26.8 - - + -
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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