Contacts of the strand formed by residues 62 - 71 (chain A) in PDB entry 6OZE
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 ARG 62 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A PHE* 3.7 5.2 - - - +
56A VAL* 3.0 32.7 + - + +
59A ASP* 3.2 19.5 + - - +
61A VAL* 1.3 84.1 - - + +
63A ALA* 1.3 61.6 + - - +
84A MET* 3.4 33.1 + - + +
85A VAL* 3.2 20.9 + - - +
86A SER* 2.8 33.9 + - - +
251A LEU* 5.8 1.1 - - + -
301A ACT 2.6 45.2 + - - +
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Residues in contact with ALA 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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53A VAL* 4.0 17.7 - - + -
54A SER 3.2 21.1 - - - +
55A PHE* 3.9 6.3 - - + +
56A VAL* 4.1 2.9 - - - +
62A ARG* 1.3 77.5 - - - +
64A CYS* 1.3 61.3 + - - +
84A MET* 3.3 13.5 - - - +
85A VAL* 2.8 33.3 + - + +
87A LEU* 4.0 19.5 - - + -
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Residues in contact with CYS 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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53A VAL* 3.2 5.4 - - - +
54A SER 2.8 30.8 + - - +
63A ALA* 1.3 75.9 - - - +
65A ALA* 1.3 62.5 + - - +
66A SER* 3.9 1.8 - - - -
82A SER* 3.8 10.5 - - - -
83A ARG 3.4 11.2 - - - -
84A MET* 4.0 2.7 - - - -
85A VAL* 4.7 0.4 - - - -
243A SER* 3.7 21.6 + - - +
246A HIS* 3.7 37.0 - - - -
247A ILE* 3.6 26.4 - - + +
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Residues in contact with ALA 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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52A ASP 3.4 4.7 - - - -
53A VAL* 4.2 7.2 - - + -
63A ALA 4.3 0.2 - - - -
64A CYS* 1.3 72.0 - - - +
66A SER* 1.3 62.5 + - - +
82A SER* 3.3 2.4 - - - -
83A ARG* 2.9 35.8 + - + +
85A VAL* 4.4 7.6 - - + +
103A PHE* 4.1 25.1 - - + -
104A LEU* 4.1 10.1 - - + -
107A LEU* 3.6 19.5 - - + +
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Residues in contact with SER 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A GLY 4.5 0.2 - - - -
51A VAL* 3.3 9.1 - - - +
52A ASP 2.8 31.4 + - - +
64A CYS* 3.9 0.2 - - - -
65A ALA* 1.3 73.3 + - - +
67A LEU* 1.3 61.0 + - - +
68A VAL 4.3 0.2 - - - -
81A GLU 3.2 5.2 - - - -
82A SER* 2.8 25.3 + - - -
104A LEU* 4.1 1.9 - - - +
107A LEU* 3.8 4.2 - - - +
239A ALA* 3.6 20.0 - - - -
242A CYS* 4.2 5.4 - - - -
243A SER* 2.6 30.9 + - - -
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Residues in contact with LEU 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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50A GLY 3.5 10.1 - - - +
51A VAL* 3.7 16.4 - - + -
66A SER* 1.3 74.2 - - - +
68A VAL* 1.3 77.7 + - - +
69A VAL* 4.8 4.0 - - + -
79A TYR* 4.1 12.2 - - + -
80A GLU* 3.4 2.3 - - - -
81A GLU* 2.9 34.7 + - + +
107A LEU* 3.6 45.9 - - + +
108A VAL* 3.9 13.5 - - + +
111A LEU* 4.0 20.9 - - + -
120A PRO* 5.1 2.0 - - + -
123A LEU* 4.3 16.4 - - + -
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Residues in contact with VAL 68 (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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49A GLY* 3.1 4.3 - - - -
50A GLY 2.9 37.8 + - - +
67A LEU* 1.3 80.5 - - - +
69A VAL* 1.3 67.0 + - - +
70A LEU* 3.7 20.2 - - + -
77A VAL* 4.9 3.6 - - + -
79A TYR 3.2 7.2 - - - +
80A GLU* 4.0 7.9 - - + +
235A PRO 3.2 27.6 - - - +
238A GLN* 4.1 6.1 - - + +
239A ALA* 3.9 16.6 - - - +
242A CYS* 3.8 30.7 - - + -
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Residues in contact with VAL 69 (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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47A ARG* 3.7 24.2 - - + -
48A VAL 3.6 8.3 - - - +
67A LEU* 4.8 2.9 - - + -
68A VAL* 1.3 78.3 - - - +
70A LEU* 1.3 64.0 + - - +
77A VAL* 3.6 3.8 - - - -
78A VAL* 2.8 35.1 + - + +
79A TYR* 2.9 26.4 + - + +
111A LEU* 3.7 22.0 - - + -
118A LEU 3.5 26.5 - - - +
120A PRO* 3.9 16.2 - - + -
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Residues in contact with LEU 70 (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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47A ARG* 3.3 5.2 - - - +
48A VAL* 2.8 38.0 + - + +
68A VAL* 3.7 26.5 - - + -
69A VAL* 1.3 81.9 - - - +
71A SER* 1.3 69.3 + - - +
75A LEU* 3.7 22.4 - - + +
76A GLU 3.1 17.0 - - - +
77A VAL* 3.9 14.1 - - + -
78A VAL* 4.4 4.0 - - - -
234A GLU* 3.7 33.0 - - + +
235A PRO* 3.8 19.3 - - + -
238A GLN* 4.5 7.0 - - + -
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Residues in contact with SER 71 (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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46A GLN 3.4 9.0 - - - -
47A ARG* 5.0 2.2 - - - -
70A LEU* 1.3 77.7 - - - +
72A PHE* 1.3 60.5 + - - +
74A GLU* 3.5 20.1 - - - +
75A LEU* 2.8 26.9 + - - +
76A GLU* 2.8 37.3 + - - +
78A VAL* 4.3 15.1 - - - +
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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