Contacts of the strand formed by residues 53 - 61 (chain A) in PDB entry 2O7R
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 VAL 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A SER* 4.4 1.9 - - - +
51A SER* 3.1 21.3 - - - -
52A PRO* 1.3 91.5 - - + +
54A LEU* 1.3 73.4 + - - +
55A THR* 4.0 4.2 + - - +
71A PHE* 3.9 16.6 - - + -
72A LEU 3.6 22.4 - - - +
73A PRO* 4.2 4.9 - - + -
74A ARG 4.2 0.2 - - - +
109A CYS* 3.5 43.1 - - + +
112A ALA* 4.3 3.6 - - + -
113A VAL* 3.5 24.2 - - + -
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Residues in contact with LEU 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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44A SER 3.4 7.6 - - - +
45A PRO 3.5 15.5 - - - +
46A ASP 3.5 24.9 - - - +
47A PRO* 3.7 18.4 - - + -
49A SER* 4.6 3.6 - - - +
51A SER 4.7 1.3 - - - +
53A VAL* 1.3 77.6 - - - +
55A THR* 1.3 66.1 + - - +
71A PHE* 3.4 0.2 - - - -
72A LEU* 2.8 51.2 + - + +
74A ARG* 3.9 16.2 - - + +
77A LEU* 4.0 26.7 - - + -
153A TRP* 3.6 21.3 - - + -
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Residues in contact with THR 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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43A ALA* 3.4 7.5 - - - +
44A SER* 2.9 39.2 + - - -
45A PRO* 3.1 25.5 - - - +
53A VAL* 4.0 6.8 + - + +
54A LEU* 1.3 79.6 - - - +
56A LYS* 1.3 61.3 + - - +
69A ARG* 4.2 12.3 - - - -
70A LEU 3.1 9.0 - - - +
71A PHE* 3.4 39.5 - - + -
105A HIS* 3.7 17.6 + - + +
153A TRP* 3.6 3.1 - - - -
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Residues in contact with LYS 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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43A ALA* 3.9 7.4 - - - -
45A PRO* 4.2 10.8 - - + -
55A THR* 1.3 75.8 - - - +
57A ASP* 1.3 64.4 + - - +
58A LEU* 4.0 17.3 + - + +
68A VAL 3.8 0.5 - - - +
69A ARG* 3.4 1.8 - - - -
70A LEU* 2.9 39.9 + - + +
151A ASP* 2.6 37.2 + - - -
152A GLU* 4.0 8.3 + - - -
153A TRP* 3.7 50.4 - - + +
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Residues in contact with ASP 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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43A ALA* 4.2 7.6 + - + +
56A LYS* 1.3 75.8 - - - +
58A LEU* 1.3 69.2 + - - +
59A ALA 4.2 0.7 + - - -
67A PHE* 3.5 24.6 - - + -
68A VAL 3.4 2.7 - - - -
69A ARG* 2.8 58.9 + - - +
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Residues in contact with LEU 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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56A LYS* 4.0 23.3 - - + +
57A ASP* 1.3 82.8 - - - +
59A ALA* 1.3 64.0 + - - +
60A LEU* 4.5 0.2 - - - -
67A PHE* 3.3 3.8 - - - +
68A VAL* 2.8 37.4 + - - +
70A LEU* 3.9 22.9 - - + -
145A TRP* 3.7 35.8 - - + -
151A ASP* 3.7 26.5 - - + +
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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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57A ASP 4.2 0.6 + - - -
58A LEU* 1.3 74.6 - - - +
60A LEU* 1.3 62.7 + - - +
61A ASN 5.4 0.2 - - - +
62A PRO* 5.8 7.2 - - + -
66A THR 4.0 6.7 - - - +
67A PHE* 4.1 4.5 - - - -
145A TRP* 3.8 15.9 + - - -
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Residues in contact with LEU 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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58A LEU 3.5 1.0 + - - -
59A ALA* 1.3 73.4 - - - +
61A ASN* 1.3 62.5 + - + +
62A PRO* 4.1 5.7 - - - +
66A THR* 2.9 37.5 + - + +
67A PHE* 3.9 7.2 - - - +
68A VAL* 4.3 11.4 - - + -
122A VAL* 4.4 7.4 - - + -
138A ASP* 4.2 9.2 - - + +
141A GLU* 4.1 15.0 - - + +
142A ALA* 4.0 26.2 - - + +
145A TRP* 3.5 49.2 - - + +
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Residues in contact with ASN 61 (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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59A ALA* 6.1 0.4 - - - -
60A LEU* 1.3 82.1 - - - +
62A PRO* 1.3 64.3 - - - +
63A LEU* 2.9 26.6 + - - +
64A HIS* 3.0 27.8 + - + -
65A ASN 2.9 22.0 + - - -
66A THR* 3.1 18.3 + - - +
141A GLU* 3.0 32.1 + - - +
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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