Contacts of the strand formed by residues 73 - 81 (chain A) in PDB entry 2QBW
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 THR 73 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A ASN* 3.6 13.5 + - - +
71A GLN 2.9 11.9 + - - +
72A ASN* 1.3 82.4 - - - +
74A VAL* 1.3 65.3 + - - +
75A GLU 4.7 0.2 - - - +
93A ARG* 3.3 53.7 + - + +
94A VAL 3.5 9.4 - - - +
95A GLU* 3.6 22.7 - - + +
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Residues in contact with VAL 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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4A LEU* 3.7 28.0 - - + -
50A ALA* 4.4 0.4 - - + -
51A ASN* 3.4 5.8 - - - +
67A LEU* 4.3 5.4 - - + -
70A PHE* 3.8 41.7 - - + -
72A ASN 4.6 0.7 - - - +
73A THR* 1.3 81.2 - - - +
75A GLU* 1.3 64.1 + - - +
76A LEU* 3.7 28.3 + - + +
93A ARG* 3.4 1.2 - - - -
94A VAL* 2.8 39.0 + - + +
96A LYS* 4.1 11.9 - - + -
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Residues in contact with GLU 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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49A GLN* 4.0 14.6 + - - +
50A ALA* 3.2 4.2 - - - +
51A ASN* 2.8 43.5 + - - +
52A GLY 4.5 7.8 + - - -
73A THR* 4.2 2.2 - - - +
74A VAL* 1.3 70.5 - - - +
76A LEU* 1.3 63.6 + - - +
77A ILE* 4.3 5.4 + - + +
91A ARG* 3.4 39.8 + - + -
92A VAL 3.3 10.5 - - - +
93A ARG* 4.3 25.3 + - + +
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Residues in contact with LEU 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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4A LEU* 5.8 0.4 - - + -
6A PHE* 4.0 13.2 - - + -
41A LEU* 3.8 30.3 - - + -
47A ILE* 4.2 20.0 - - + -
49A GLN 3.5 1.6 - - - -
50A ALA* 3.6 26.5 - - + -
67A LEU* 4.2 10.5 - - + -
74A VAL* 3.9 17.5 - - + +
75A GLU* 1.3 74.2 - - - +
77A ILE* 1.3 63.1 + - - +
78A ILE* 4.0 9.4 - - + -
90A ILE 3.6 0.7 - - - +
91A ARG* 3.3 4.7 - - - +
92A VAL* 2.9 42.3 + - + +
94A VAL* 3.9 18.6 - - + -
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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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47A ILE* 3.7 0.9 - - - -
48A ILE* 2.9 37.5 + - + +
49A GLN* 2.9 51.1 + - + +
75A GLU* 5.1 5.4 - - + +
76A LEU* 1.3 76.0 - - - +
78A ILE* 1.3 64.4 + - - +
89A GLU* 3.5 38.6 - - + +
90A ILE 3.4 6.5 - - - +
91A ARG* 3.9 39.3 - - + +
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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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28A VAL* 5.2 0.2 - - + -
41A LEU* 4.0 23.6 - - + -
45A ASP* 3.5 39.3 - - + +
46A LYS 3.0 8.7 - - - +
47A ILE* 4.0 24.2 - - + -
76A LEU* 4.3 11.7 - - + -
77A ILE* 1.3 78.6 - - - +
79A VAL* 1.3 72.7 + - - +
80A ARG* 3.8 10.8 - - + +
89A GLU* 3.3 5.9 - - - +
90A ILE* 2.8 59.4 + - + +
92A VAL* 5.4 1.8 - - + -
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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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44A GLY 4.3 2.3 - - - +
45A ASP* 3.7 2.8 - - - -
46A LYS* 2.8 44.1 + - + +
48A ILE* 3.9 33.4 - - + -
78A ILE* 1.3 78.4 - - - +
80A ARG* 1.3 62.7 + - - +
81A GLU 4.4 0.3 + - - -
87A LYS* 4.2 29.4 - - + -
88A GLN 3.4 9.9 - - - +
89A GLU* 4.8 7.9 - - + +
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Residues in contact with ARG 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 LEU 3.3 23.0 + - - -
41A LEU* 4.0 0.4 - - - +
42A GLN* 3.5 38.7 + - - +
44A GLY 5.5 0.9 - - - -
45A ASP* 2.8 43.5 + - - +
78A ILE* 3.8 8.0 - - + +
79A VAL* 1.3 73.9 - - - +
81A GLU* 1.3 73.7 + - - +
82A VAL* 3.8 6.6 + - + +
87A LYS* 3.3 6.5 - - - +
88A GLN* 2.8 46.3 + - - +
90A ILE* 3.7 30.0 - - + +
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Residues in contact with GLU 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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20A ARG* 2.6 47.9 + - - +
42A GLN* 5.1 3.6 + - - -
44A GLY 5.8 0.4 + - - -
79A VAL 4.4 0.6 + - - -
80A ARG* 1.3 83.2 - - - +
82A VAL* 1.3 59.3 + - - +
83A GLY* 2.7 33.3 - - - +
85A GLY* 4.8 3.1 + - - +
86A ALA 3.5 6.5 - - - +
87A LYS* 3.4 24.3 + - - +
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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