Contacts of the strand formed by residues 73 - 80 (chain A) in PDB entry 5TOL
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 GLN 73 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A THR* 3.2 5.3 - - - -
68A VAL* 2.8 46.2 + - + +
71A PRO 4.0 7.4 + - - +
72A PRO* 1.3 73.2 - - - +
74A THR* 1.3 63.2 + - - +
75A LEU* 3.6 7.3 + - + +
99A TYR 4.0 4.0 - - - +
100A TYR* 3.6 14.8 - - - -
101A GLN* 2.7 54.5 + - - +
104A LEU* 4.0 17.4 - - + +
105A SER* 4.0 19.2 - - - -
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Residues in contact with THR 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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65A GLU* 3.5 38.7 + - + +
66A MET 3.4 5.8 - - - +
67A THR* 4.3 10.1 - - + +
72A PRO* 4.0 3.5 + - - +
73A GLN* 1.3 70.8 - - - +
75A LEU* 1.3 71.5 + - - +
76A ASN* 5.3 1.8 - - - +
98A ARG* 3.5 23.7 - - - +
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Residues in contact with LEU 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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65A GLU* 3.5 2.8 - - - +
66A MET* 2.8 35.3 + - + +
68A VAL* 3.7 33.0 - - + -
73A GLN* 4.0 8.5 - - + +
74A THR* 1.3 84.9 - - - +
76A ASN* 1.3 64.5 + - - +
77A ILE* 4.0 14.9 + - + -
88A VAL* 4.1 28.7 - - + -
89A GLY 5.3 0.4 - - - +
98A ARG* 4.2 6.7 - - + +
99A TYR* 3.8 38.1 - - - +
100A TYR* 3.9 6.5 - - + +
164A GLU* 3.6 13.2 - - + +
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Residues in contact with ASN 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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63A TYR* 3.4 25.2 - - + -
64A VAL 3.6 2.5 - - - -
65A GLU* 3.9 18.5 - - - +
74A THR* 5.3 1.7 - - - +
75A LEU* 1.3 75.8 - - - +
77A ILE* 1.3 66.0 + - - +
98A ARG* 3.4 14.3 - - - +
162A ASN* 3.0 48.7 + - - +
163A TRP* 3.9 2.5 - - - -
164A GLU* 2.9 36.3 + - - +
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Residues in contact with ILE 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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63A TYR* 3.2 5.2 - - - +
64A VAL* 2.9 35.9 + - + +
66A MET* 3.8 28.7 - - + -
68A VAL* 6.5 0.2 - - + -
75A LEU* 4.2 20.2 - - + +
76A ASN* 1.3 83.0 - - - +
78A LEU* 1.3 63.6 + - - +
79A VAL 3.3 0.7 + - - -
86A PHE* 4.1 4.9 - - + -
88A VAL* 3.6 22.2 - - + -
164A GLU 4.4 0.4 - - - -
165A GLY* 3.3 23.8 - - - +
166A ILE 3.4 6.3 - - - +
167A LEU* 3.3 41.3 - - + +
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Residues in contact with LEU 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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60A GLN 4.0 7.6 - - - +
61A GLY* 3.6 15.0 - - - -
62A TYR 3.4 32.5 - - - +
63A TYR* 3.9 4.6 - - - +
77A ILE* 1.3 69.7 - - - +
79A VAL* 1.3 65.9 + - - +
80A ASP* 3.5 5.4 + - + -
163A TRP* 3.9 23.4 - - + +
165A GLY 2.8 16.2 + - - +
166A ILE* 3.6 16.4 - - + +
167A LEU* 2.7 33.3 + - - +
278A GLY* 4.8 0.4 - - - -
501A 7H3 3.4 51.4 - - + +
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Residues in contact with VAL 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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54A LEU* 4.1 11.7 - - + -
62A TYR* 2.9 23.3 + - + +
64A VAL* 3.9 33.9 - - + +
77A ILE 4.0 2.2 - - - +
78A LEU* 1.3 75.6 - - - +
80A ASP* 1.3 60.7 + - - +
167A LEU* 4.1 8.7 - - + -
169A LEU* 3.9 19.7 - - + -
200A LEU* 4.0 24.0 - - + -
202A LEU* 5.8 1.1 - - + -
222A MET* 4.1 12.6 - - - -
277A SER* 3.0 31.9 + - - +
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Residues in contact with ASP 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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78A LEU* 3.5 2.7 + - + -
79A VAL* 1.3 74.6 - - - +
81A THR* 1.3 62.0 + - - +
82A GLY 2.9 13.0 + - - -
83A SER* 2.7 19.7 + - - +
166A ILE* 3.1 23.9 - - + +
167A LEU 2.9 16.3 + - - +
168A GLY* 3.4 2.8 - - - -
169A LEU* 2.9 24.1 + - - -
276A ASP* 3.2 5.0 - - - +
277A SER* 3.6 0.9 - - - -
278A GLY* 3.3 9.3 - - - +
501A 7H3 2.7 47.9 + - - -
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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