Contacts of the strand formed by residues 70 - 76 (chain A) in PDB entry 4FPR
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 MET 70 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A THR* 3.9 19.7 - - + +
55A LEU* 3.7 40.2 - - - +
56A ILE* 3.8 20.1 - - + +
59A SER* 4.0 0.4 - - - -
66A TRP* 3.4 30.5 - - + +
67A GLY 3.3 24.0 - - - +
68A ILE 3.6 3.6 + - - -
69A ASP* 1.3 82.8 + - - +
71A THR* 1.3 69.8 + - - +
94A ILE* 4.0 19.3 - - + -
95A THR 3.3 5.4 - - - +
96A ALA* 4.1 11.2 - - + -
131A TRP* 4.3 4.5 - - + -
42B THR* 3.4 10.2 + - - +
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Residues in contact with THR 71 (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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49A ASN* 5.5 0.4 - - - -
52A THR* 4.8 2.5 - - - -
70A MET* 1.3 82.0 - - - +
72A ALA* 1.3 62.1 + - - +
73A LYS* 5.6 1.4 - - - +
93A LYS 3.8 0.9 - - - +
94A ILE* 3.5 3.6 - - - -
95A THR* 2.9 33.6 + - - -
97A HIS* 2.7 31.1 + - - +
41B LYS* 4.0 29.4 - - + +
42B THR* 4.2 5.4 - - + +
45B LEU* 4.2 21.1 - - + -
74B VAL* 6.0 1.6 - - + -
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Residues in contact with ALA 72 (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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45A LEU* 3.8 12.3 - - + +
48A CYS* 3.8 21.3 - - - -
49A ASN* 3.3 31.9 + - - +
52A THR* 3.4 14.1 - - - +
71A THR* 1.3 74.9 - - - +
73A LYS* 1.3 67.9 + - - +
93A LYS 3.6 4.9 - - - +
94A ILE* 4.4 2.7 - - + +
45B LEU* 4.8 11.9 - - - +
73B LYS* 5.7 1.4 - - - +
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Residues in contact with LYS 73 (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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45A LEU* 4.3 5.2 - - - -
48A CYS* 3.8 3.8 - - - -
71A THR 5.6 1.6 - - - +
72A ALA* 1.3 78.8 - - - +
74A VAL* 1.3 64.0 + - - +
93A LYS* 3.1 44.2 + - + +
95A THR* 6.0 2.5 - - - +
73B LYS* 4.1 42.0 - - + +
74B VAL 5.9 2.5 - - - -
75B GLN* 5.4 7.5 + - - +
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Residues in contact with VAL 74 (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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41A LYS* 4.7 4.7 - - + +
44A ALA* 4.2 9.6 - - + +
45A LEU* 3.5 40.8 - - + +
48A CYS* 4.4 10.1 - - + -
73A LYS* 1.3 78.0 - - - +
75A GLN* 1.3 78.3 + - - +
76A CYS* 4.3 4.9 - - - -
90A CYS* 3.9 18.2 - - + -
91A THR 3.2 16.8 - - - +
92A CYS* 4.4 3.8 - - + -
71B THR* 6.1 1.6 - - + -
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Residues in contact with GLN 75 (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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74A VAL* 1.3 77.8 - - - +
76A CYS* 1.3 62.3 + - - +
90A CYS* 3.3 2.8 - - - +
91A THR* 2.8 38.1 + - - +
134D ASN* 4.9 6.7 + - - +
136D LYS* 3.5 37.4 - - + +
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Residues in contact with CYS 76 (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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39A PRO* 5.5 2.0 - - + -
41A LYS* 4.0 29.0 + - + +
44A ALA* 3.7 19.1 - - - -
74A VAL* 4.3 3.8 - - - -
75A GLN* 1.3 75.1 - - - +
77A ALA* 1.3 71.5 + - - +
78A PRO* 3.9 1.4 - - - +
88A VAL* 4.6 4.0 - - + -
89A LEU 3.6 4.0 - - - -
90A CYS* 2.0 46.7 - - - -
136D LYS* 3.8 14.3 - - - +
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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