Contacts of the strand formed by residues 75 - 83 (chain A) in PDB entry 2O3B
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 75 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A TYR* 3.6 9.8 - - - -
70A ASN* 3.0 28.7 + - - +
73A LYS* 3.2 17.1 - - - +
74A GLY* 1.3 85.2 - - - +
76A ALA* 1.3 71.7 + - - +
115A TYR* 4.5 0.2 - - - +
144A MET 5.5 1.3 - - - -
145A THR 5.3 1.3 - - - -
147A MET 3.7 22.0 - - - +
148A MET* 4.3 7.6 - - + -
149A PRO* 4.2 7.2 - - + -
182A PRO* 3.9 10.3 - - + +
194A VAL* 3.7 21.1 - - + -
195A THR 4.1 10.4 + - - +
197A PRO* 6.0 0.2 - - + -
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Residues in contact with ALA 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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67A LEU* 3.8 17.3 - - + -
68A SER 3.2 13.5 - - - +
69A TYR* 4.2 3.1 - - - +
70A ASN* 4.8 0.8 - - - +
73A LYS* 5.3 1.0 - - - +
75A THR* 1.3 85.2 + - - +
77A ASN* 1.3 61.9 + - - +
78A TRP 3.6 15.9 - - - +
79A VAL* 3.8 14.6 - - + -
125A ILE* 4.3 7.7 - - + +
145A THR 3.9 9.4 + - - +
147A MET 4.9 1.2 + - - -
182A PRO* 3.2 23.4 - - - +
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Residues in contact with ASN 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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56A ASP 2.8 24.4 + - - -
57A ASN* 3.7 4.9 + - - +
68A SER* 2.7 27.8 + - - +
69A TYR 3.6 4.4 + - - -
70A ASN* 2.8 32.4 + - - +
73A LYS* 4.7 9.4 + - - +
76A ALA* 1.3 73.2 - - - +
78A TRP* 1.3 74.9 + - + +
182A PRO* 4.0 15.0 - - - +
201A TRP* 3.5 15.9 - - - -
254A TYR* 3.2 28.3 + - + +
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Residues in contact with TRP 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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40A LEU* 3.7 29.6 - - + -
44A ASN* 3.4 24.0 - - - -
45A PRO* 3.5 21.5 - - + -
46A SER* 2.9 26.4 + - - +
48A ALA* 4.5 0.2 - - + -
59A LEU* 4.1 17.3 - - + -
66A ALA 3.8 6.5 - - - -
67A LEU* 3.2 20.5 - - - +
68A SER* 3.1 44.0 + - - -
76A ALA* 3.2 3.2 - - - +
77A ASN* 1.3 91.9 - - + +
79A VAL* 1.3 69.0 + - - +
80A ALA* 3.8 14.4 - - + -
179A VAL* 4.2 6.1 - - + -
180A ALA 3.2 13.5 - - - +
181A GLY* 4.2 2.0 - - - -
201A TRP* 3.7 15.3 - - + -
254A TYR* 4.0 13.7 - + - -
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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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65A TYR* 3.8 25.8 - - + -
66A ALA 3.4 11.4 - - - +
67A LEU* 3.8 11.0 - - + -
76A ALA* 3.8 6.3 - - + -
78A TRP* 1.3 81.3 - - - +
80A ALA* 1.3 63.3 + - - +
81A TRP* 3.4 18.6 - - + -
125A ILE* 3.5 37.2 - - + -
126A ALA* 4.2 1.8 - - + -
145A THR 4.7 4.7 - - - +
146A ASN* 3.9 14.4 - - - +
179A VAL* 3.3 1.8 - - - -
180A ALA 2.8 29.0 + - - -
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Residues in contact with ALA 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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39A HIS* 3.5 21.6 - - - +
40A LEU* 4.2 6.3 - - + -
43A GLY 5.7 2.2 - - - +
45A PRO* 5.9 0.7 - - + -
65A TYR* 3.5 1.4 - - - +
66A ALA 2.8 32.3 + - - +
78A TRP* 3.8 18.7 - - + -
79A VAL* 1.3 74.4 - - - +
81A TRP* 1.3 64.4 + - - +
178A ILE 3.0 9.2 - - - +
179A VAL* 4.1 12.1 - - + -
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Residues in contact with TRP 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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39A HIS* 3.7 12.2 + - - -
64A GLN 4.0 0.2 - - - +
65A TYR* 3.8 12.6 - - + -
79A VAL* 3.4 31.4 - - + -
80A ALA* 1.3 76.3 - - - +
82A GLN* 1.3 74.1 + - - +
83A LEU* 4.0 1.5 + - + -
125A ILE* 3.2 31.6 - - + -
126A ALA* 4.1 8.1 - - + -
127A PRO* 3.3 22.6 - - + +
130A ASP* 3.0 25.7 + - + -
131A ARG* 3.5 23.1 - - + +
177A TYR* 4.7 0.9 - - - -
178A ILE* 2.7 77.4 + - + +
180A ALA* 4.2 3.8 - - + -
202A LYS* 4.1 16.6 - - - -
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Residues in contact with GLN 82 (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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38A VAL* 4.0 20.4 - - + +
39A HIS* 3.2 18.0 + - - +
81A TRP* 1.3 74.1 - - - +
83A LEU* 1.3 64.2 + - - +
84A ASN* 3.6 16.2 + - - +
86A SER* 5.4 0.2 + - - -
87A TRP* 2.8 33.4 + - - +
131A ARG* 2.9 26.9 + - - -
175A GLU* 3.3 13.1 + - - +
176A LEU 3.5 7.9 - - - +
177A TYR* 3.0 44.1 + - + -
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Residues in contact with LEU 83 (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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81A TRP* 4.5 1.8 - - + -
82A GLN* 1.3 75.7 - - - +
84A ASN* 1.3 68.9 + - - +
87A TRP* 4.3 0.9 - - + -
88A LEU* 4.4 12.8 - - + -
130A ASP* 3.4 58.1 - - + +
131A ARG* 3.9 5.2 - - - +
166A CYS* 4.4 6.3 - - + +
167A ARG* 4.4 10.5 - - + -
170A VAL* 3.7 23.2 - - + +
175A GLU* 3.6 1.6 - - - +
176A LEU* 2.7 49.3 + - + +
178A ILE* 4.1 23.6 - - + -
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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