Contacts of the strand formed by residues 35 - 42 (chain B) in PDB entry 3NCF
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 ASN 35 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B PRO* 3.5 2.1 - - - +
34B THR* 1.3 89.9 - - - +
36B TYR* 1.3 89.1 + - - +
37B SER* 5.6 1.4 + - - -
81B ALA* 3.4 5.0 - - - +
82B THR* 2.8 46.9 + - - +
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Residues in contact with TYR 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B PRO* 4.4 9.0 - - + -
24B TRP* 3.5 42.4 - + + -
26B PRO* 3.1 34.4 - - + +
33B PRO* 3.4 21.1 - - + +
35B ASN* 1.3 94.9 + - - +
37B SER* 1.3 61.8 + - - +
38B LEU 4.3 0.2 - - - -
50B GLU* 5.2 0.2 - - - +
54B TYR* 4.1 10.8 + - + -
60B ASN* 3.2 26.9 + - - -
79B VAL* 4.1 6.7 - - + -
80B ASN* 3.1 17.0 - - - -
81B ALA* 3.7 18.2 - - + -
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Residues in contact with SER 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ASN* 5.6 1.2 + - - -
36B TYR* 1.3 75.5 + - - +
38B LEU* 1.3 60.4 + - - +
39B THR* 3.9 9.7 + - - +
50B GLU* 2.9 23.6 + - - -
54B TYR* 3.3 2.9 - - - -
78B MET 3.8 0.9 - - - +
79B VAL* 3.3 4.1 - - - -
80B ASN* 2.8 57.9 + - - -
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Residues in contact with LEU 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ILE* 4.0 25.4 - - + -
22B CYS* 5.0 4.5 - - + -
24B TRP* 4.1 26.0 - - + -
37B SER* 1.3 73.6 - - - +
39B THR* 1.3 70.5 + - - +
40B TYR* 4.1 12.8 - - + -
50B GLU* 3.6 1.4 - - - +
51B CYS* 2.9 35.6 + - + -
54B TYR* 2.7 14.5 + - - +
62B CYS* 4.0 32.1 - - + -
64B PHE* 4.1 13.7 - - + -
77B MET* 4.4 14.1 - - + -
78B MET 3.4 10.1 - - - +
79B VAL* 4.2 3.6 - - + +
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Residues in contact with THR 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B SER* 3.9 15.6 + - - +
38B LEU* 1.3 81.1 - - - +
40B TYR* 1.3 63.3 + - - +
48B MET* 4.3 24.0 - - + +
49B HIS 3.2 14.1 - - - +
50B GLU* 4.5 7.6 - - + -
77B MET* 3.4 0.9 - - - +
78B MET* 2.8 54.3 + - - +
80B ASN* 5.4 6.5 + - - +
89B PHE* 6.0 0.7 - - - -
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Residues in contact with TYR 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B LEU* 4.1 8.1 - - + -
39B THR* 1.3 78.0 - - - +
41B HIS* 1.3 72.1 + - - +
42B ARG* 4.0 14.8 - - - -
48B MET* 3.7 3.5 - - - +
49B HIS* 2.9 74.3 + + + +
50B GLU 3.7 16.6 + - - -
51B CYS* 4.0 1.6 - - - -
52B PRO* 4.6 0.9 - - - +
64B PHE* 3.6 29.7 - + - -
68B TYR* 4.0 24.8 + - - +
75B TYR* 3.8 23.1 - + - -
76B ILE 3.0 15.5 - - - +
77B MET* 3.6 16.8 - - + -
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Residues in contact with HIS 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ILE* 6.0 1.8 - - + -
40B TYR* 1.3 82.2 - - - +
42B ARG* 1.3 69.1 + - - +
45B GLU 4.4 8.9 + - - +
46B THR* 5.0 3.1 - - - +
47B LEU 3.1 26.9 - - - +
48B MET* 4.4 12.1 - - + -
49B HIS* 4.8 1.6 - - - -
75B TYR* 3.7 1.4 - - - -
76B ILE* 2.7 75.8 + - + +
92B GLU* 4.4 7.0 + - - -
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Residues in contact with ARG 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B TYR* 4.0 12.1 - - + -
41B HIS* 1.3 80.6 + - - +
43B GLU* 1.3 64.3 + - - +
44B GLY 3.5 0.2 + - - -
45B GLU* 3.3 46.3 + - - +
47B LEU 4.8 1.0 + - - -
49B HIS* 4.9 4.7 - - + +
68B TYR* 4.0 8.5 + - - +
70B SER* 2.5 31.1 + - - -
73B ARG* 3.4 48.3 - - - +
74B THR 3.4 5.8 + - - +
75B TYR* 3.1 58.7 + - - -
76B ILE* 4.2 3.1 - - - -
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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