Contacts of the strand formed by residues 51 - 61 (chain B) in PDB entry 2ORY
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 ASP 51 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50B ASP* 1.3 75.8 + - - +
52B TRP* 1.3 62.0 + - - +
78B LYS* 3.4 2.3 - - - -
79B LYS* 2.5 80.9 + - + +
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Residues in contact with TRP 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LEU* 3.7 27.3 - - + +
12B PHE* 3.7 30.7 - + - -
41B LEU* 3.6 27.8 - - + +
46B PRO 5.1 0.8 + - - -
47B PHE* 3.4 37.5 + - + +
50B ASP* 3.7 21.9 + - + +
51B ASP* 1.3 81.4 + - - +
53B GLU* 1.3 62.8 + - - +
76B ILE* 3.8 18.6 - - + -
77B GLN 3.5 5.8 - - - -
78B LYS* 3.4 60.1 - - + -
84B GLU* 4.7 7.9 - - + -
86B VAL* 4.3 16.4 - - + -
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Residues in contact with GLU 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LEU* 4.3 2.7 - - - -
52B TRP* 1.3 77.9 - - - +
54B VAL* 1.3 78.1 + - - +
55B VAL* 3.2 16.7 + - + +
76B ILE* 3.6 4.5 - - - -
77B GLN* 2.8 36.2 + - + +
79B LYS* 2.8 39.9 - - + +
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Residues in contact with VAL 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B MET* 5.1 1.1 - - + -
34B LEU* 4.1 23.3 - - + -
37B MET* 4.5 13.2 - - + -
38B LYS* 5.6 3.1 - - + +
41B LEU* 4.1 19.2 - - + +
53B GLU* 1.3 84.0 - - - +
55B VAL* 1.3 60.2 + - - +
56B TRP 3.7 10.3 - - - +
57B GLY 3.3 29.4 - - - +
58B PRO* 4.3 2.7 - - + -
74B TYR* 4.4 17.7 - - + -
75B VAL 3.5 8.3 - - - +
76B ILE* 4.1 7.6 - - + -
146B PRO* 3.6 12.9 - - + +
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Residues in contact with VAL 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B GLU* 3.2 19.0 + - - +
54B VAL* 1.3 76.8 - - - +
56B TRP* 1.3 59.6 + - - +
75B VAL* 2.9 27.0 + - + +
77B GLN* 3.4 44.6 - - + +
85B TYR* 4.5 1.3 - - + -
146B PRO* 3.4 16.3 - - - +
147B GLY 3.6 4.9 + - - -
155B PHE* 3.4 37.4 - - + -
159B LYS* 4.2 6.3 - - - +
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Residues in contact with TRP 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B VAL* 3.7 2.6 - - - +
55B VAL* 1.3 78.9 - - - +
57B GLY* 1.3 69.5 + - - +
59B ALA* 4.0 17.3 - - + -
73B MET* 3.6 53.2 - - + -
74B TYR* 3.4 9.1 - - - +
75B VAL* 3.0 47.6 + - + -
139B LEU* 3.5 20.4 - - + -
141B PRO* 3.5 12.2 - - + +
146B PRO* 3.6 3.3 - - - +
147B GLY* 3.8 12.6 - - - -
150B LYS 2.8 29.4 + - - -
151B THR 3.7 6.3 + - - -
152B ILE* 3.6 16.6 - - + -
155B PHE* 3.4 36.8 - + + +
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Residues in contact with GLY 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B VAL* 3.3 4.4 - - - +
56B TRP* 1.3 82.8 - - - +
58B PRO* 1.4 75.8 - - - +
59B ALA 3.5 3.1 - - - -
73B MET 4.2 0.2 - - - -
141B PRO* 3.5 12.6 - - - +
145B ILE* 3.1 20.5 - - - +
146B PRO* 3.0 25.6 + - - +
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Residues in contact with PRO 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B ALA* 3.6 38.0 - - + +
33B ILE* 3.9 17.5 - - + -
34B LEU* 3.7 35.0 - - + +
37B MET* 4.0 13.5 - - + -
54B VAL* 4.3 1.8 - - + -
57B GLY* 1.4 82.4 - - - +
59B ALA* 1.3 58.1 + - - +
60B VAL* 5.0 1.1 - - + -
72B MET* 3.7 22.2 - - + -
73B MET 3.6 7.0 - - - +
74B TYR* 3.9 2.7 - - + -
141B PRO* 4.9 1.4 - - - +
142B LYS 5.2 0.3 + - - -
145B ILE* 3.6 12.3 - - + +
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Residues in contact with ALA 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B ALA* 5.5 0.9 - - - -
56B TRP* 4.0 27.4 - - + -
57B GLY* 3.5 0.4 - - - -
58B PRO* 1.3 73.5 - - - +
60B VAL* 1.3 60.9 + - - +
72B MET* 3.3 4.0 - - - -
73B MET 3.1 29.0 + - - -
139B LEU* 3.6 22.5 - - + +
140B LYS 4.2 1.8 - - - +
141B PRO* 4.1 23.8 - - + -
142B LYS 5.7 0.2 - - - +
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Residues in contact with VAL 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B LYS 3.4 19.7 - - - +
28B LYS* 4.9 8.5 - - + +
30B ALA* 5.2 10.8 - - + +
33B ILE* 4.0 20.6 - - + -
58B PRO 5.0 2.2 - - - -
59B ALA* 1.3 76.6 - - - +
61B TYR* 1.3 60.8 - - - +
62B THR* 3.2 23.6 + - - +
71B ALA 3.5 9.0 - - - +
72B MET* 3.6 24.2 - - + -
90B ARG* 4.5 8.1 - - - +
139B LEU* 3.7 11.4 - - - +
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Residues in contact with TYR 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A LEU* 4.7 5.4 - - - +
60B VAL* 1.3 72.9 - - - +
62B THR* 1.3 68.3 + - - +
63B MET* 3.0 40.3 - - + +
69B ASN* 3.3 43.6 - - + +
70B ASP* 3.4 2.4 - - - -
71B ALA* 2.9 39.6 + - + +
135B THR* 3.7 37.4 - - + +
139B LEU* 4.1 19.7 - - + +
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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