Contacts of the strand formed by residues 71 - 80 (chain A) in PDB entry 3F40
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 ASP 71 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A GLU* 3.4 6.7 - - - +
68A GLU* 2.9 38.9 + - + +
69A GLY 3.2 1.2 + - - -
70A ASN* 1.3 83.0 + - - +
72A VAL* 1.3 63.3 + - - +
73A CYS 4.3 0.2 - - - -
90A LEU* 4.1 22.5 - - + +
91A TYR 3.3 4.9 - - - +
92A HIS* 2.7 37.3 + - - +
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Residues in contact with VAL 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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7A THR 4.5 4.3 - - - +
8A ARG* 4.7 0.7 - - + -
11A VAL* 4.0 23.3 - - + -
65A MSE 3.5 28.5 - - + -
66A PHE 3.3 11.9 - - - +
67A GLU* 3.6 28.3 - - + +
71A ASP* 1.3 77.4 - - - +
73A CYS* 1.3 60.8 + - - +
74A LEU* 3.9 15.5 - - + -
89A GLY 3.6 1.4 - - - +
90A LEU* 3.5 4.3 - - - +
91A TYR* 2.8 38.7 + - + +
93A LEU* 4.0 14.1 - - + -
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Residues in contact with CYS 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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65A MSE 3.6 0.7 - - - -
66A PHE* 2.9 56.1 + - + +
72A VAL* 1.3 73.4 - - - +
74A LEU* 1.3 63.3 + - - +
75A ILE* 5.0 4.3 - - - -
88A SER* 3.2 28.0 - - - -
89A GLY 3.2 13.5 - - - -
90A LEU* 4.4 17.0 - - + -
104A TYR* 6.1 1.1 - - - -
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Residues in contact with LEU 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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11A VAL* 3.8 8.5 - - + -
12A LEU* 4.7 3.1 - - + -
15A ILE* 3.7 28.0 - - + -
62A VAL* 4.3 14.4 - - + -
64A LYS 3.5 3.8 - - - +
65A MSE 3.6 41.1 - - + -
72A VAL* 3.9 9.2 - - + -
73A CYS* 1.3 73.6 - - - +
75A ILE* 1.3 62.3 + - - +
76A TYR* 3.8 25.8 + - + -
88A SER* 3.3 6.6 + - - -
89A GLY 2.8 37.5 + - - +
91A TYR* 3.7 24.7 - - + -
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Residues in contact with ILE 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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62A VAL* 3.7 0.9 - - - +
63A HIS* 2.8 37.1 + - + +
64A LYS* 2.9 31.7 + - + +
66A PHE* 3.9 27.1 - - + -
73A CYS* 5.0 2.5 - - - -
74A LEU* 1.3 70.3 - - - +
76A TYR* 1.3 62.5 + - - +
87A ALA 3.7 6.3 - - - +
88A SER* 3.7 28.3 - - - +
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Residues in contact with TYR 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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15A ILE* 4.1 2.7 - - + -
60A TYR* 3.6 35.7 - + + -
61A VAL 3.1 21.1 - - - +
62A VAL* 3.8 6.3 - - + -
63A HIS* 4.3 3.4 - - - -
74A LEU* 3.8 28.0 - - + -
75A ILE* 1.3 77.1 - - - +
77A ASP* 1.3 67.9 + - - +
78A ILE* 3.9 17.6 + - + -
86A ALA* 3.8 1.1 - - - -
87A ALA* 2.9 46.1 + - + +
88A SER 4.1 0.2 - - - -
89A GLY* 3.5 32.7 - - - -
91A TYR* 2.7 29.1 + - - -
101A LEU* 4.1 5.2 - - - +
103A VAL* 4.0 9.3 - - + +
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Residues in contact with ASP 77 (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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59A LYS 3.6 0.9 - - - +
60A TYR* 3.3 5.2 - - - +
61A VAL* 2.9 41.3 + - + +
63A HIS* 3.0 29.0 + - + -
76A TYR* 1.3 73.4 - - - +
78A ILE* 1.3 60.7 + - - +
84A THR* 3.9 23.7 - - + +
85A ILE 3.4 2.9 - - - -
86A ALA* 3.6 23.0 - - - +
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Residues in contact with ILE 78 (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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58A PHE* 3.9 14.1 - - + -
59A LYS 3.3 9.2 - - - +
60A TYR* 3.7 31.2 - - + +
76A TYR* 3.9 18.8 - - + -
77A ASP* 1.3 76.5 - - - +
79A ASN* 1.3 62.3 + - - +
80A MSE 3.4 34.0 + - + +
83A LYS 3.3 3.6 - - - +
84A THR* 3.4 2.4 - - - -
85A ILE* 2.8 41.6 + - + +
87A ALA* 3.7 26.0 - - + -
103A VAL* 4.2 11.2 - - + -
105A PHE* 4.8 4.3 - - + -
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Residues in contact with ASN 79 (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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57A LYS 4.6 1.2 - - - +
58A PHE* 3.5 9.4 - - - +
59A LYS* 2.8 45.3 + - + +
77A ASP 4.1 0.8 - - - -
78A ILE* 1.3 69.0 - - - +
80A MSE 1.3 59.0 + - - +
81A ASN 3.8 2.4 + - - -
82A GLY* 3.0 32.6 + - - -
83A LYS 3.3 6.3 - - - -
84A THR* 4.1 16.5 + - + +
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Residues in contact with MSE 80 (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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40A MSE 3.7 16.6 - - + -
58A PHE* 3.4 39.9 - - + -
78A ILE* 3.5 34.1 - - + +
79A ASN* 1.3 69.8 - - - +
81A ASN* 1.3 73.5 + - - +
82A GLY 3.1 0.4 - - - -
83A LYS* 2.7 28.9 + - - +
85A ILE* 4.4 11.4 - - + -
105A PHE* 3.9 24.5 - - + -
110A LEU* 3.6 37.5 - - + +
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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