Contacts of the strand formed by residues 75 - 80 (chain A) in PDB entry 4N2F
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 THR 75 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A VAL* 4.1 15.1 + - - +
30A TYR* 5.1 1.4 - - - +
40A PHE* 4.0 21.0 - - + -
52A VAL* 3.8 26.7 - - + -
53A VAL 3.2 4.7 - - - +
54A ARG* 3.4 22.8 - - + +
69A TRP* 4.7 4.5 - - + -
70A LEU 4.2 12.6 + - - +
72A SER* 3.0 27.5 + - - +
74A SER* 1.3 78.4 + - - +
76A THR* 1.3 65.2 + - - +
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Residues in contact with THR 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A TRP* 3.9 30.2 - - + +
27A THR 3.5 11.7 - - - +
28A ASP* 4.6 7.2 - - + +
29A VAL* 5.0 4.5 - - - +
30A TYR* 6.5 0.2 - - + -
52A VAL* 3.6 5.7 - - - +
53A VAL* 2.8 46.2 + - - +
73A PRO 3.9 16.6 - - - +
74A SER 4.6 2.0 + - - -
75A THR* 1.3 81.7 - - - +
77A LEU* 1.3 72.3 + - - +
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Residues in contact with LEU 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 6.2 0.4 - - + -
26A TRP* 3.4 6.1 - - - +
27A THR* 2.8 49.1 + - + +
29A VAL* 3.6 24.5 - - + -
40A PHE* 4.2 13.0 - - + -
42A LEU* 3.7 23.3 - - + -
50A VAL* 4.1 9.0 - - + -
51A GLU 3.3 4.5 - - - +
52A VAL* 3.9 14.4 - - + -
53A VAL* 4.7 1.1 - - - -
76A THR* 1.3 86.0 + - - +
78A ARG* 1.3 60.6 - - - +
79A VAL* 4.2 7.6 - - + -
93A VAL* 4.1 26.5 - - + -
95A VAL* 4.1 10.1 - - + -
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Residues in contact with ARG 78 (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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4A GLU* 4.3 7.4 + - - +
24A TYR* 3.4 43.2 + - + -
25A LEU 3.4 4.7 - - - +
26A TRP* 5.3 0.7 - - + -
49A TRP 3.6 1.0 - - - +
50A VAL* 3.4 4.3 - - - -
51A GLU* 2.7 75.2 + - + +
53A VAL* 4.0 20.7 - - + +
56A GLY 5.9 1.4 + - - -
58A ALA* 3.3 21.4 - - - +
77A LEU* 1.3 74.9 - - - +
79A VAL* 1.3 63.1 + - - +
80A THR* 4.2 5.3 + - - +
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Residues in contact with VAL 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A TYR* 3.6 6.0 - - + -
24A TYR* 3.5 3.1 - - - +
25A LEU* 2.9 48.4 + - + -
27A THR* 3.8 20.4 - - - +
48A VAL* 3.6 27.1 - - + -
49A TRP 3.4 2.9 - - - +
50A VAL* 4.5 11.0 - - + -
77A LEU* 4.2 16.4 - - + -
78A ARG* 1.3 77.0 - - - +
80A THR* 1.3 65.4 + - - +
93A VAL* 4.3 9.0 - - + -
111A LEU* 4.7 5.2 - - + -
113A LEU* 4.0 19.1 - - + -
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Residues in contact with THR 80 (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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19A TYR* 3.3 9.4 - - - +
23A THR 5.1 0.4 - - - +
24A TYR* 3.9 13.8 - - + +
48A VAL* 3.7 0.3 - - - -
49A TRP* 2.8 70.4 + - + +
51A GLU* 4.5 6.6 + - - -
78A ARG* 4.5 10.0 - - - +
79A VAL* 1.3 76.9 + - - +
81A MET* 1.3 76.1 + - - +
82A SER* 5.7 0.2 - - - -
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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