Contacts of the strand formed by residues 68 - 78 (chain A) in PDB entry 2DB9
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 GLY 68 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A ALA* 5.4 0.2 - - - -
44A THR* 3.1 14.9 + - - -
66A ILE* 3.4 8.0 - - - +
67A THR* 1.3 84.9 + - - +
69A VAL* 1.3 69.4 + - - +
88A GLN* 3.0 32.7 + - - -
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Residues in contact with VAL 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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39A PHE* 3.9 11.4 - - + -
40A ALA* 3.2 42.9 - - + +
43A VAL* 3.3 16.2 - - + -
68A GLY* 1.3 79.0 - - - +
70A VAL* 1.3 76.1 + - - +
85A LYS* 3.8 31.6 - - + -
86A GLY 3.7 6.3 - - - +
87A LEU* 4.0 6.3 - - + -
88A GLN* 4.1 2.3 + - - +
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Residues in contact with VAL 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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69A VAL* 1.3 84.6 - - - +
71A GLU* 1.3 65.2 + - - +
72A THR* 4.9 4.5 - - + -
85A LYS* 3.6 5.0 - - - +
86A GLY* 2.9 50.3 + - - +
88A GLN* 3.1 35.0 - - + +
97A VAL* 3.8 23.8 - - + -
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Residues in contact with GLU 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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70A VAL* 1.3 79.7 - - - +
72A THR* 1.3 67.3 + - - +
84A ASN* 3.9 13.8 + - - +
85A LYS* 6.0 1.1 - - + -
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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 VAL* 4.9 5.4 - - + -
71A GLU* 1.3 83.2 - - - +
73A ALA* 1.3 61.4 + - - +
74A LYS 3.1 19.9 + - - -
84A ASN* 3.3 35.5 + - - -
86A GLY* 4.2 19.7 - - - +
97A VAL* 5.3 3.6 - - + -
99A ARG* 3.9 31.8 + - - +
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Residues in contact with ALA 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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72A THR* 1.3 75.9 - - - +
74A LYS* 1.3 69.3 + - + +
75A VAL* 4.0 5.9 + - - +
84A ASN* 5.5 0.2 - - - -
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Residues in contact with LYS 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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72A THR* 3.1 21.6 + - - -
73A ALA* 1.3 85.8 - - + +
75A VAL* 1.3 66.3 + - - +
76A TYR* 4.3 1.7 + - - -
84A ASN* 3.9 3.8 - - - +
99A ARG* 4.3 14.8 + - - +
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Residues in contact with VAL 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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73A ALA 4.7 5.6 - - - +
74A LYS* 1.3 78.0 - - - +
76A TYR* 1.3 65.5 + - - +
82A ARG* 3.3 47.1 - - + +
83A THR 3.3 10.8 - - - +
84A ASN* 3.4 25.8 - - + -
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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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72A THR* 5.0 0.4 - - - -
74A LYS 4.4 4.3 - - - -
75A VAL* 1.3 79.2 - - - +
77A GLN* 1.3 70.9 + - - +
78A LEU* 4.3 2.2 - - + -
82A ARG* 3.1 8.6 - - - +
83A THR* 3.0 64.9 + - + +
84A ASN* 4.2 7.4 - - - -
85A LYS 2.9 24.8 + - - -
99A ARG* 3.1 42.0 - - + -
100A LEU* 3.2 23.6 + - + +
101A GLU* 3.1 28.9 - - - +
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Residues in contact with GLN 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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76A TYR* 1.3 86.6 - - - +
78A LEU* 1.3 63.4 + - - +
79A GLY 4.0 3.1 - - - +
80A GLY* 3.5 36.4 + - - +
81A THR 3.4 4.9 - - - +
82A ARG* 3.9 12.1 - - + +
101A GLU* 3.4 16.4 + - - +
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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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27A ARG* 3.4 29.8 - - + +
31A GLU* 3.2 44.3 - - + +
34A CYS* 4.8 1.3 - - + -
76A TYR* 4.3 1.6 - - + -
77A GLN* 1.3 78.2 - - - +
79A GLY* 1.3 61.3 + - - +
80A GLY 3.3 0.7 - - - -
81A THR* 2.5 23.7 + - + +
83A THR* 3.9 20.0 - - + -
100A LEU* 3.3 50.9 - - + -
101A GLU* 3.6 11.9 - - - +
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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