Contacts of the strand formed by residues 71 - 80 (chain A) in PDB entry 2QCB
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 71 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A ASP* 2.5 29.8 + - - +
17A ILE* 4.5 7.2 - - + -
60A TYR* 4.2 11.7 - - + -
61A ASP* 3.3 28.7 - - + +
64A PRO* 3.6 14.2 - - + +
69A SER 4.9 0.9 + - - -
70A GLY* 1.3 72.6 - - - -
72A ALA* 1.3 69.9 + - - +
73A LEU* 3.8 2.4 - - - +
95A GLN* 3.1 3.0 - - - -
96A TYR* 2.8 48.3 + - - +
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Residues in contact with ALA 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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60A TYR* 3.4 1.4 - - - +
61A ASP* 2.9 39.0 + - + +
70A GLY 4.0 3.2 + - - -
71A THR* 1.3 74.5 - - - +
73A LEU* 1.3 60.9 + - - +
94A GLY 3.4 9.9 - - - +
95A GLN* 4.3 3.5 - - + +
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Residues in contact with LEU 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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17A ILE* 4.4 23.8 - - + -
29A PHE* 5.7 0.9 - - + -
39A LEU* 4.2 15.0 - - + -
59A ARG 3.3 14.1 - - - +
60A TYR* 3.6 8.3 - - + +
71A THR 3.8 2.5 - - - +
72A ALA* 1.3 76.4 - - - +
74A GLY* 1.3 60.2 + - - +
75A TRP* 4.4 13.0 - - + -
93A SER* 3.7 4.2 + - - -
94A GLY* 2.9 58.4 + - - +
95A GLN* 3.5 14.1 - - - +
96A TYR* 4.5 4.9 - - + -
104A ILE* 4.0 31.2 - - + -
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Residues in contact with GLY 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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39A LEU* 3.6 2.4 - - - +
58A GLY* 3.2 1.8 - - - -
59A ARG 2.9 32.5 + - - +
73A LEU* 1.3 77.2 - - - +
75A TRP* 1.3 69.0 + - - +
92A TRP 3.0 13.2 - - - -
93A SER* 4.4 2.2 - - - -
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Residues in contact with TRP 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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29A PHE* 3.5 44.3 - + - -
39A LEU* 4.5 10.3 - - + -
43A TYR* 3.9 7.4 - + - -
56A LEU* 4.1 28.9 - - + -
57A THR 3.4 15.9 - - - +
58A GLY* 3.8 5.4 - - - -
73A LEU* 4.4 9.9 - - + -
74A GLY* 1.3 82.0 - - - +
76A THR* 1.3 65.7 + - - +
77A VAL* 4.4 0.4 - - + -
91A THR* 3.2 5.1 - - - -
92A TRP* 2.9 86.3 + + + +
94A GLY 6.0 0.2 - - - -
104A ILE* 4.3 9.2 - - + -
106A THR* 3.9 12.6 - - + -
130A PHE* 3.8 30.1 - + - -
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Residues in contact with THR 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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55A VAL 4.0 0.3 - - - +
56A LEU* 3.2 25.8 - - - +
57A THR* 2.9 20.7 + - - +
75A TRP* 1.3 73.7 - - - +
77A VAL* 1.3 75.5 + - - +
78A ALA* 4.4 2.5 - - + +
89A ALA* 4.5 9.6 - - + -
90A THR 3.3 11.7 - - - +
91A THR* 3.3 23.6 - - + +
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Residues in contact with VAL 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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43A TYR* 3.6 27.8 - - + -
54A TYR* 3.6 27.6 - - + -
55A VAL 3.9 6.5 - - - +
56A LEU* 3.7 13.2 - - + -
75A TRP* 4.4 0.4 - - + -
76A THR* 1.3 82.4 - - - +
78A ALA* 1.3 65.1 + - - +
79A TRP* 3.7 26.2 + - + -
89A ALA* 3.2 3.1 - - - +
90A THR 2.9 33.2 + - - +
92A TRP* 3.7 20.8 - - + -
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Residues in contact with ALA 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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54A TYR* 3.8 4.2 - - - +
55A VAL 4.5 4.9 + - - +
76A THR* 4.3 3.5 - - + +
77A VAL* 1.3 79.4 - - - +
79A TRP* 1.3 59.3 + - - +
80A LYS* 2.8 24.2 + - + +
88A SER 3.6 7.6 - - - +
89A ALA* 4.1 9.0 - - + -
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Residues in contact with TRP 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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43A TYR* 3.7 27.1 - + - -
45A SER* 4.0 22.7 - - - -
49A ASN 4.9 1.0 - - - +
50A ALA* 4.2 2.2 - - + -
54A TYR* 3.5 45.1 + + + -
77A VAL* 3.7 20.0 - - + -
78A ALA* 1.3 68.2 - - - +
80A LYS* 1.3 56.9 + - - +
84A ARG 3.8 0.7 - - - +
85A ASN* 3.4 4.9 + - - -
86A ALA* 2.9 32.5 + - + +
87A HIS 5.1 0.2 - - - -
88A SER* 2.8 53.1 + - - +
89A ALA* 3.9 3.4 - - - -
90A THR* 2.9 23.6 + - - +
92A TRP* 3.8 12.1 - + - -
110A LEU* 4.6 0.6 - - + +
400A KYS 3.6 45.2 - - + +
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Residues in contact with LYS 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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54A TYR* 3.7 5.9 - - - +
55A VAL 5.5 1.6 + - - -
78A ALA* 2.8 19.3 + - + +
79A TRP* 1.3 76.1 - - - +
81A ASN* 1.3 75.7 + - - +
82A ASN* 5.7 2.4 + - - -
84A ARG 3.5 3.8 - - - -
85A ASN* 3.7 33.0 - - + +
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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