Contacts of the strand formed by residues 68 - 77 (chain A) in PDB entry 4OBZ
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 VAL 68 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A THR 3.8 10.1 - - - +
67A TYR* 1.3 84.4 - - - +
69A LYS* 1.3 70.8 + - + +
70A ASN 3.7 0.2 + - - -
89A GLN* 2.8 66.0 + - + +
112B ARG* 5.9 1.8 - - + -
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Residues in contact with LYS 69 (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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67A TYR* 3.4 30.2 - - + +
68A VAL* 1.3 82.8 - - + +
70A ASN* 1.3 60.4 + - - +
71A GLY 5.3 0.2 - - - +
400A NAG 4.4 5.2 - - - +
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Residues in contact with ASN 70 (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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67A TYR* 4.6 0.4 + - - -
68A VAL 3.7 2.0 + - - +
69A LYS* 1.3 75.6 - - - +
71A GLY* 1.3 59.7 + - - +
72A THR* 2.8 36.6 + - - -
87A LEU* 3.3 27.4 + - + +
88A SER* 4.0 6.9 - - - +
89A GLN* 5.1 2.5 - - + +
400A NAG 1.4 81.3 + - - +
114B VAL* 4.9 4.8 - - + +
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Residues in contact with GLY 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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67A TYR* 5.7 0.6 + - - -
69A LYS* 5.3 0.8 - - - +
70A ASN* 1.3 73.9 - - - +
72A THR* 1.4 64.5 + - - +
73A SER* 3.4 5.7 + - - -
86A TYR* 3.6 22.1 - - - +
87A LEU 3.0 13.9 + - - -
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Residues in contact with THR 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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70A ASN* 2.8 23.0 + - - -
71A GLY* 1.4 72.6 - - - +
73A SER* 1.3 71.4 + - - +
86A TYR* 3.3 0.2 - - - -
87A LEU* 2.7 47.4 + - + +
400A NAG 3.5 22.2 + - - +
145B ASN* 4.2 14.4 - - - +
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Residues in contact with SER 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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71A GLY 3.4 5.1 + - - -
72A THR* 1.3 84.4 - - - +
74A PHE* 1.3 61.4 + - - +
85A GLY 3.4 11.2 + - - -
86A TYR* 4.2 2.5 - - - +
145B ASN* 4.1 9.0 + - - +
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Residues in contact with PHE 74 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A TRP* 4.3 3.8 - - + -
72A THR 3.8 0.2 + - - -
73A SER* 1.3 75.4 - - - +
75A ASP* 1.3 65.2 + - - +
76A ILE* 3.6 30.1 - - + -
83A LEU* 3.6 36.1 - - + -
84A SER* 3.2 14.3 - - - -
85A GLY* 2.9 65.5 + - - +
86A TYR 3.5 12.8 - - - -
87A LEU* 4.1 17.7 - - + -
116B GLY* 3.6 27.6 - - - -
117B GLU 3.8 5.4 - - - -
118B ALA* 4.2 4.3 - - - -
144B VAL* 4.7 5.4 - - + -
145B ASN* 4.4 11.4 - - + +
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Residues in contact with ASP 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 PHE* 1.3 73.8 - - - +
76A ILE* 1.3 61.2 + - - +
77A HIS* 3.5 27.9 + - - +
83A LEU 3.5 10.1 - - - +
84A SER* 3.7 16.1 - - - -
144B VAL* 3.9 18.8 - - - +
145B ASN* 5.0 0.8 + - - -
172D ASP* 5.4 4.0 - - - +
174D ASP* 3.4 22.8 - - - +
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Residues in contact with ILE 76 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A ASN* 4.1 24.2 - - + +
40A TRP* 3.7 23.3 - - + -
74A PHE* 3.6 26.2 - - + -
75A ASP* 1.3 77.2 - - - +
77A HIS* 1.3 65.0 + - - +
78A TYR* 3.4 45.5 - - + +
82A SER* 2.9 16.8 + - - -
83A LEU* 2.8 31.2 + - + +
144B VAL* 4.1 20.9 - - + -
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Residues in contact with HIS 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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75A ASP* 3.5 35.5 + - - +
76A ILE* 1.3 73.0 - - - +
78A TYR* 1.3 67.1 + - - +
81A GLY 3.9 0.7 - - - -
82A SER* 2.8 21.6 + - - +
174D ASP* 3.3 34.1 - - + +
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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