Contacts of the strand formed by residues 52 - 63 (chain A) 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 TRP 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A LEU* 3.8 33.0 - - + -
12A PHE* 3.8 19.1 - + - -
41A LEU* 3.9 29.6 + - + +
46A PRO 4.7 1.6 + - - -
47A PHE* 3.8 40.6 + + + +
50A ASP* 3.6 29.8 + - + +
51A ASP* 1.3 81.6 + - - +
53A GLU* 1.3 64.9 + - - +
76A ILE* 3.5 27.8 - - + -
77A GLN 3.6 2.7 - - - -
78A LYS* 3.8 47.3 - - + -
79A LYS* 4.5 2.1 - - - +
84A GLU* 4.5 8.1 - - - -
86A VAL* 4.2 16.2 - - + -
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Residues in contact with GLU 53 (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 LYS* 5.5 7.1 + - - -
41A LEU* 4.7 0.7 - - - -
52A TRP* 1.3 79.7 - - - +
54A VAL* 1.3 75.4 + - - +
55A VAL* 3.2 21.3 + - + +
76A ILE* 3.4 3.4 - - - -
77A GLN* 2.8 39.6 + - + +
79A LYS* 3.7 31.3 + - + -
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Residues in contact with VAL 54 (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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34A LEU* 4.0 19.7 - - + -
37A MET* 4.3 22.0 - - + -
38A LYS* 5.1 9.8 - - + -
41A LEU* 3.8 23.3 - - + +
53A GLU* 1.3 86.0 + - - +
55A VAL* 1.3 58.7 + - - +
56A TRP 4.1 3.4 - - - +
57A GLY 3.4 29.8 - - - +
58A PRO* 4.5 2.9 - - + -
74A TYR* 4.6 13.9 - - + -
75A VAL 3.6 10.5 - - - +
76A ILE* 4.5 3.8 - - + +
146A PRO* 3.7 12.5 - - + +
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Residues in contact with VAL 55 (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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53A GLU* 3.6 25.6 - - + +
54A VAL* 1.3 74.8 - - - +
56A TRP* 1.3 59.7 + - - +
75A VAL* 3.0 25.1 + - + +
77A GLN* 3.3 42.6 - - + +
85A TYR* 4.3 2.5 - - + -
146A PRO* 3.7 9.1 - - - +
147A GLY 3.7 9.5 + - - -
155A PHE* 3.3 36.6 - - + -
159A LYS* 4.7 3.8 - - - -
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Residues in contact with TRP 56 (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 VAL* 3.7 1.5 - - - +
55A VAL* 1.3 80.1 - - - +
57A GLY* 1.3 63.4 + - - +
59A ALA* 3.4 18.4 - - + -
73A MET* 3.2 55.0 - - + -
74A TYR* 3.1 11.9 - - - +
75A VAL* 2.8 53.0 + - + +
139A LEU* 3.8 14.4 - - + -
141A PRO* 3.4 15.1 - - + +
146A PRO* 3.6 4.0 - - - +
147A GLY* 3.6 17.2 + - - -
150A LYS 3.0 29.6 + - - -
151A THR 3.9 0.4 + - - -
152A ILE* 3.8 16.8 - - + -
155A PHE* 3.4 38.6 - + + +
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Residues in contact with GLY 57 (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 VAL* 3.4 4.3 - - - +
56A TRP* 1.3 85.7 - - - +
58A PRO* 1.3 76.5 - - - +
59A ALA 3.4 4.3 - - - -
74A TYR* 4.3 0.4 - - - -
141A PRO* 3.6 4.2 - - - +
145A ILE* 3.3 8.3 - - - +
146A PRO* 2.9 38.6 + - - +
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Residues in contact with PRO 58 (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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30A ALA* 3.2 48.2 - - + +
33A ILE* 3.9 9.4 - - + -
34A LEU* 3.8 33.7 - - + +
37A MET* 4.1 9.0 - - - -
54A VAL* 4.5 1.6 - - + -
57A GLY* 1.3 80.0 - - - +
59A ALA* 1.3 59.4 + - - +
60A VAL* 3.9 1.6 - - + -
72A MET* 3.7 31.9 - - + -
73A MET 3.7 5.6 - - - +
74A TYR* 3.9 4.2 - - + -
141A PRO* 4.6 1.7 - - - +
142A LYS 5.3 0.2 + - - -
145A ILE* 3.7 9.3 - - + +
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Residues in contact with ALA 59 (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 TRP* 3.4 32.8 - - + -
57A GLY* 3.4 1.0 - - - -
58A PRO* 1.3 71.9 - - - +
60A VAL* 1.3 60.4 + - - +
72A MET* 3.4 5.0 - - - +
73A MET 3.0 27.1 + - - -
139A LEU* 3.7 21.7 - - + +
140A LYS 4.2 3.4 - - - +
141A PRO* 4.1 21.1 - - + -
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Residues in contact with VAL 60 (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 LYS* 5.3 7.4 - - - +
29A ASN 5.1 1.6 - - - +
30A ALA* 3.9 27.3 - - + +
33A ILE* 4.0 15.7 - - + -
58A PRO 3.9 3.0 + - - +
59A ALA* 1.3 76.8 - - - +
61A TYR* 1.3 63.3 + - - +
62A THR* 3.5 34.0 + - + +
71A ALA 3.6 8.3 - - - +
72A MET* 3.9 16.6 - - + -
90A ARG* 4.4 8.7 - - - +
139A LEU* 3.8 8.6 - - - +
142A LYS* 4.9 17.5 + - - +
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Residues in contact with TYR 61 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A VAL* 1.3 72.1 - - - +
62A THR* 1.3 72.2 + - - +
63A MET* 4.2 37.2 - - + +
69A ASN* 3.5 23.1 - - + -
70A ASP* 3.4 4.4 - - - -
71A ALA* 2.8 39.7 + - + +
135A THR* 4.7 19.1 - - + -
139A LEU* 3.9 17.2 - - + +
264B LEU* 4.6 12.3 - - - +
265B LEU* 5.1 12.0 - - + +
266B TYR* 3.6 39.8 + + + +
267B GLN* 4.7 2.2 + - - -
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Residues in contact with THR 62 (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 LYS* 3.5 32.4 + - - +
60A VAL* 3.5 22.0 + - + +
61A TYR* 1.3 89.5 - - - +
63A MET* 1.3 76.6 + - - +
64A PRO* 4.8 0.5 - - - +
70A ASP* 3.0 28.7 - - + +
90A ARG* 4.9 5.2 - - - +
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Residues in contact with MET 63 (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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61A TYR* 4.2 34.0 - - + +
62A THR* 1.3 85.7 - - - +
64A PRO* 1.3 76.8 - - + +
66A THR* 2.9 36.9 + - + +
70A ASP* 4.4 1.8 + - - -
264B LEU* 3.7 36.1 - - + -
267B GLN* 5.4 2.2 - - - +
303B GLU* 4.5 12.8 - - - +
305B LEU* 5.2 4.0 - - + -
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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