Contacts of the helix formed by residues 60 - 71 (chain B) in PDB entry 4WFN
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 60 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54B LYS* 4.3 4.7 - - - +
58B LYS 3.6 2.9 + - - +
59B VAL* 1.3 74.4 - - - +
61B LYS* 1.3 63.7 + - - +
62B PRO* 3.5 26.4 - - + +
63B MET* 3.7 23.0 - - + +
64B GLN* 2.9 26.4 + - - +
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Residues in contact with LYS 61 (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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59B VAL 3.9 1.0 + - - -
60B ASN* 1.3 70.9 - - - +
62B PRO* 1.4 72.1 - - + +
64B GLN* 3.3 19.7 + - - +
65B GLY* 3.0 18.5 + - - -
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Residues in contact with PRO 62 (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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60B ASN* 3.5 24.0 - - + +
61B LYS* 1.4 95.4 - - + +
63B MET* 1.3 60.7 + - + +
65B GLY* 3.0 5.8 + - - -
66B HIS* 2.9 23.1 + - - +
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Residues in contact with MET 63 (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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54B LYS* 5.5 6.1 - - - +
59B VAL* 3.8 18.6 - - + -
60B ASN* 3.5 20.4 + - + +
61B LYS 3.4 0.4 - - - -
62B PRO* 1.3 79.9 - - + +
64B GLN* 1.3 59.1 + - - +
66B HIS* 3.1 18.1 + - + +
67B PHE* 2.9 47.6 + - + -
75B THR 5.6 1.6 - - - +
78B LEU* 4.2 25.8 - - + -
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Residues in contact with GLN 64 (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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56B GLU* 2.8 41.2 - - - +
57B ARG 4.6 0.7 - - - +
59B VAL* 2.9 28.2 + - + +
60B ASN 2.9 21.9 + - - +
61B LYS* 3.4 22.7 - - - +
63B MET* 1.3 76.3 - - - +
65B GLY* 1.3 58.5 + - - +
67B PHE* 3.6 5.8 + - + +
68B ALA* 2.9 29.3 + - - +
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Residues in contact with GLY 65 (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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61B LYS 3.0 13.6 + - - -
62B PRO* 3.0 6.4 + - - -
64B GLN* 1.3 75.1 - - - +
66B HIS* 1.3 64.8 - - - +
68B ALA* 3.0 8.1 + - - +
69B LYS* 3.0 24.8 + - - +
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Residues in contact with HIS 66 (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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34B VAL* 4.2 11.1 + - + +
35B GLN* 3.2 34.3 + - + -
48B GLN* 3.4 22.9 + - - -
62B PRO 2.9 11.2 + - - +
63B MET* 3.1 24.8 + - + +
65B GLY* 1.3 72.8 - - - +
67B PHE* 1.3 68.5 + + + +
69B LYS* 3.0 35.2 + - - +
70B ALA* 3.8 3.6 + - - +
78B LEU* 4.1 20.9 - - + -
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Residues in contact with PHE 67 (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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34B VAL* 4.0 19.5 - - + -
54B LYS* 5.6 1.1 - - + -
59B VAL* 4.7 14.4 - - + -
63B MET* 2.9 35.6 + - + +
64B GLN* 4.1 5.4 - - + +
66B HIS* 1.3 81.1 - - + +
68B ALA* 1.3 50.8 + - - +
70B ALA* 3.5 1.4 + - - -
71B GLY* 2.7 33.6 + - - -
72B VAL* 3.3 11.8 + - + +
73B ALA 3.1 27.6 - - - +
74B PRO* 3.7 7.0 - - + -
75B THR* 3.3 50.9 - - + -
78B LEU* 3.7 28.9 - - + -
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Residues in contact with ALA 68 (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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64B GLN 2.9 20.0 + - - +
65B GLY* 3.0 10.7 + - - +
67B PHE* 1.3 75.1 - - - +
69B LYS* 1.3 67.6 + - - +
71B GLY* 2.8 15.6 + - - +
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Residues in contact with LYS 69 (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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34B VAL 5.5 4.5 + - - +
35B GLN* 4.3 25.9 + - - +
65B GLY 3.0 13.7 + - - +
66B HIS* 3.0 23.1 + - - +
68B ALA* 1.3 76.9 - - - +
70B ALA* 1.3 59.5 + - + +
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Residues in contact with ALA 70 (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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33B ILE 3.9 14.4 - - - +
34B VAL* 3.2 30.5 - - - +
66B HIS 3.8 1.9 + - - +
67B PHE 3.5 4.7 + - - +
69B LYS* 1.3 78.6 - - - +
71B GLY* 1.3 66.8 + - - +
72B VAL* 4.4 8.1 - - + +
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Residues in contact with GLY 71 (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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67B PHE 2.7 12.2 + - - -
68B ALA* 2.8 14.7 + - - -
70B ALA* 1.3 80.2 - - - +
72B VAL* 1.3 61.9 + - - +
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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