Contacts of the strand formed by residues 60 - 67 (chain A) in PDB entry 2OZ6
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 GLU 60 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A LEU* 4.9 9.9 - - + -
53A ILE 3.4 7.9 - - - +
54A GLU* 3.8 15.8 - - + +
58A GLY 3.4 14.2 - - - +
59A ARG* 1.3 73.9 - - - +
61A MET* 1.3 61.6 + - - +
92A ARG* 3.4 29.8 + - - -
179A ARG* 3.4 35.6 + - - +
302A CMP 3.1 35.8 + - - +
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Residues in contact with MET 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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52A LEU* 3.2 5.5 - - - -
53A ILE* 2.7 53.6 + - + +
54A GLU* 5.8 0.2 - - - -
59A ARG 4.3 0.2 + - - -
60A GLU* 1.3 73.4 - - - +
62A ILE* 1.3 72.1 + - - +
63A ILE* 3.3 10.1 + - + -
135A LYS* 3.8 17.9 - - - -
139A LEU* 4.0 23.1 - - + -
179A ARG 3.2 9.6 - - - +
180A ILE 4.0 2.9 - - - +
181A VAL 3.7 11.4 - - - +
182A GLY* 3.5 33.7 - - - +
302A CMP 4.7 6.7 - - + +
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Residues in contact with ILE 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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50A THR* 3.8 19.7 - - + -
51A ILE 3.3 3.6 - - - -
52A LEU* 3.4 22.0 - - + -
61A MET* 1.3 71.9 - - - +
63A ILE* 1.3 53.7 + - - +
64A GLY* 3.7 18.4 - - - +
65A TYR* 4.1 10.1 - - + +
92A ARG* 5.9 0.9 - - - +
135A LYS* 2.7 30.5 + - - -
176A GLU* 3.1 47.1 - - - +
179A ARG* 3.0 28.2 + - + +
180A ILE* 3.7 21.5 - - + +
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Residues in contact with ILE 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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51A ILE* 2.7 22.2 + - + +
53A ILE* 3.7 48.7 - - + -
61A MET* 4.0 8.7 - - + +
62A ILE* 1.3 73.6 - - - +
64A GLY* 1.3 58.6 + - - +
131A LYS* 6.2 0.3 - - - +
132A THR* 4.4 12.2 + - + +
135A LYS* 4.1 30.5 + - + +
301A CMP 3.2 42.8 + - + +
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Residues in contact with GLY 64 (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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50A THR* 3.6 3.3 - - - -
51A ILE* 2.8 34.7 + - - +
62A ILE* 3.4 9.2 - - - +
63A ILE* 1.3 82.9 - - - +
65A TYR* 1.3 66.7 + - - +
131A LYS* 6.4 1.8 - - - -
301A CMP 5.7 4.7 - - - -
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Residues in contact with TYR 65 (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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48A SER* 5.6 0.2 - - - +
49A VAL 3.2 8.5 - - - +
50A THR* 3.7 29.4 - - + -
51A ILE* 4.7 0.2 - - - -
62A ILE* 4.1 6.2 - - + +
64A GLY* 1.3 77.9 - - - -
66A LEU* 1.3 72.8 + - - +
67A ASN* 4.0 8.0 + - - +
94A LYS* 3.7 31.3 - - + +
131A LYS* 5.9 3.5 - - - +
155A LEU* 3.7 25.8 - - + +
158A GLN* 3.5 34.7 + - - +
172A ILE* 4.6 1.4 - - - +
176A GLU* 2.6 42.2 + - - +
180A ILE* 3.5 16.5 - - + +
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Residues in contact with LEU 66 (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 ILE* 3.7 4.2 - - + +
48A SER* 3.4 5.2 + - - -
49A VAL* 3.0 40.8 + - + +
51A ILE* 3.7 24.0 - - + -
65A TYR* 1.3 81.5 - - - +
67A ASN* 1.3 64.5 + - - +
70A ASP* 3.5 18.2 - - + +
71A PHE 3.9 0.7 - - - +
72A PHE* 3.7 27.6 - - + -
128A ARG* 3.6 48.7 - - + +
301A CMP 4.4 8.7 - - + +
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Residues in contact with ASN 67 (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 ILE* 3.4 7.5 - - - +
47A GLY 3.6 8.7 - - - +
48A SER* 2.3 25.9 + - - +
65A TYR* 4.0 5.0 + - - +
66A LEU* 1.3 80.5 + - - +
68A SER* 1.3 72.4 + - - +
70A ASP* 2.7 30.6 + - - +
94A LYS* 5.9 0.9 + - - -
158A GLN* 3.7 21.8 + - - +
159A PRO* 3.1 33.5 - - + +
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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