Contacts of the strand formed by residues 62 - 68 (chain A) in PDB entry 3OFN
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 LYS 62 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A LEU* 4.3 20.6 - - + -
55A VAL 3.3 11.2 - - - +
56A GLU* 3.6 28.1 + - - -
57A PHE* 4.6 4.3 - - - -
60A GLY 3.8 7.7 + - - +
61A VAL* 1.3 84.1 - - - +
63A GLY* 1.3 53.8 + - - +
77A LEU* 3.6 1.7 - - - +
78A PHE* 2.6 56.0 + - + +
93A THR* 5.3 6.3 - - + -
113A LEU* 5.6 4.3 - - + -
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Residues in contact with GLY 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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54A LEU* 3.4 6.8 - - - +
55A VAL* 2.7 34.5 + - - +
57A PHE* 4.2 2.3 - - - -
62A LYS* 1.3 74.7 - - - +
64A MET* 1.3 62.0 + - - -
75A ILE* 3.8 13.9 - - - -
76A VAL 3.1 15.0 - - - -
77A LEU* 4.1 2.0 - - - -
78A PHE* 4.1 8.1 - - - -
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Residues in contact with MET 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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52A GLU* 3.3 36.6 - - + +
53A GLU 3.6 6.3 - - - +
54A LEU* 4.2 2.7 - - + -
63A GLY* 1.3 76.9 - - - +
65A ALA* 1.3 61.6 + - - +
66A LEU* 3.3 26.5 + - + -
75A ILE* 3.8 4.0 - - - -
76A VAL* 3.0 46.4 + - + +
78A PHE* 3.9 14.0 - - + -
97A VAL* 3.2 35.2 - - + -
243A PRO* 5.7 1.3 - - - -
246A TYR* 5.3 6.3 - - + -
247A LEU* 3.9 20.6 - - + -
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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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49A ILE* 3.7 25.4 - - + -
50A GLN 4.2 7.6 - - - +
51A ALA* 4.1 2.0 - - - -
52A GLU* 2.7 32.4 + - - -
53A GLU 2.9 18.4 + - - +
55A VAL* 5.1 0.6 - - + +
64A MET* 1.3 68.2 - - - +
66A LEU* 1.3 61.2 + - - +
67A ILE 3.7 0.7 - - - -
68A LEU* 4.5 4.9 - - + -
73A VAL* 3.9 17.9 - - + -
74A GLY 3.8 6.1 - - - -
75A ILE* 3.8 6.6 - - + +
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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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51A ALA* 5.7 4.3 - - - +
52A GLU* 4.4 12.1 - - + +
64A MET* 3.3 38.7 + - + +
65A ALA* 1.3 74.7 - - - +
67A ILE* 1.3 65.1 + - + +
68A LEU* 4.2 2.0 + - - -
74A GLY 3.2 7.3 + - - +
76A VAL* 3.8 31.6 - - + -
246A TYR* 5.4 8.5 - - + +
283A LEU* 3.9 22.2 - - + -
287A LEU* 4.2 19.3 - - + -
289A ARG* 4.6 20.0 + - - +
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Residues in contact with ILE 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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66A LEU* 1.3 88.6 - - + +
68A LEU* 1.3 66.3 + - - +
69A GLU* 3.9 29.6 + - + +
73A VAL* 3.3 9.9 - - - +
74A GLY* 2.9 39.2 + - - +
287A LEU* 3.7 46.0 - - + +
289A ARG* 4.6 18.2 - - + +
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Residues in contact with LEU 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 ILE* 3.8 37.5 - - + +
50A GLN* 4.7 0.4 - - - -
51A ALA* 3.9 33.9 - - + +
65A ALA* 4.5 9.0 - - + +
66A LEU 4.2 1.7 + - - -
67A ILE* 1.3 80.2 - - - +
69A GLU* 1.3 65.0 + - - +
70A PRO* 4.9 0.2 - - - +
72A GLN 4.5 2.2 - - - -
73A VAL* 3.9 13.5 - - + -
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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