Contacts of the strand formed by residues 78 - 83 (chain A) in PDB entry 3F7F
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 LEU 78 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A GLY* 5.3 5.8 - - - +
71A HIS 3.6 0.5 - - - +
72A PHE* 3.0 9.3 - - - -
73A SER* 2.8 47.6 + - - +
76A SER 3.6 0.2 - - - -
77A THR* 1.3 84.4 + - - +
79A LEU* 1.3 64.1 + - - +
80A THR* 3.9 14.6 - - - +
94A ASN* 3.9 15.0 - - + +
95A ILE 3.5 28.5 - - - +
96A HIS* 3.5 36.1 - - + +
97A LEU* 4.8 0.4 - - - -
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Residues in contact with LEU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A TYR* 5.1 5.6 - - + -
71A HIS 3.4 8.5 - - - +
72A PHE* 3.5 31.4 - - + -
78A LEU* 1.3 74.1 - - - +
80A THR* 1.3 62.8 + - - +
81A PHE* 3.6 32.5 - - + -
93A ILE 3.6 0.7 - - - +
94A ASN* 3.5 2.3 - - - -
95A ILE* 2.6 51.0 + - + +
97A LEU* 5.1 5.1 - - + +
108A LEU* 3.8 17.7 - - + -
110A ILE* 4.4 8.3 - - + -
119A VAL* 3.8 25.6 - - + -
121A VAL* 5.5 0.9 - - + -
131A LEU* 4.4 9.9 - - + -
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Residues in contact with THR 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A GLY* 4.6 8.7 + - - -
69A CYS 4.2 0.2 - - - -
70A TYR* 2.9 30.3 - - - +
71A HIS* 2.9 25.6 + - + -
78A LEU* 3.9 12.1 - - - +
79A LEU* 1.3 76.4 + - - +
81A PHE* 1.3 72.5 + - - +
82A TYR* 4.8 10.7 - - + -
92A THR* 4.7 10.1 - - - +
93A ILE 3.2 5.4 - - - +
94A ASN* 2.9 27.4 + - - +
478A PRO* 5.6 5.8 - - + -
479A TYR* 5.5 2.2 - - - +
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Residues in contact with PHE 81 (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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68A ILE* 4.2 14.4 - - + -
69A CYS 3.2 6.7 - - - +
70A TYR* 3.7 24.2 - + + -
79A LEU* 3.6 33.7 - - + -
80A THR* 1.3 75.6 - - - +
82A TYR* 1.3 63.1 + - - +
91A LYS 3.8 1.0 - - - +
92A THR* 2.8 6.5 - - - -
93A ILE* 2.6 59.2 + - + +
95A ILE* 3.5 31.2 - - + -
110A ILE* 4.3 9.9 - - + -
117A LEU* 3.6 28.3 - - + -
119A VAL* 4.2 9.6 - - + -
133A LEU* 3.8 12.6 - - + -
138A LEU* 4.5 7.0 - - + -
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Residues in contact with TYR 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 3.9 14.6 - - + -
68A ILE* 3.4 6.6 - - - +
69A CYS* 2.7 62.3 + - + -
71A HIS* 3.9 14.1 + + - -
80A THR* 4.8 9.4 - - + -
81A PHE* 1.3 78.4 - - - +
83A PRO* 1.3 74.5 - - + +
87A ALA* 4.4 3.6 - - + -
91A LYS 3.9 1.3 - - - -
92A THR* 3.4 23.1 - - + -
478A PRO* 4.0 13.2 - - + -
479A TYR* 2.9 55.5 + + + -
481A HIS* 2.8 24.9 + - - -
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Residues in contact with PRO 83 (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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66A GLU* 5.0 4.9 - - - +
67A TYR 3.5 7.2 - - - +
68A ILE* 3.7 6.5 - - + -
82A TYR* 1.3 88.0 - - + +
84A LEU* 1.3 67.6 + - - +
85A SER 3.2 1.3 - - - +
86A ASP* 3.2 38.4 + - + +
87A ALA* 3.3 13.1 + - - +
90A GLY* 4.1 9.2 - - - -
91A LYS 3.4 20.2 - - - +
138A LEU 5.1 3.6 - - - +
139A PHE* 4.1 28.0 - - + -
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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