Contacts of the helix formed by residues 59 - 68 (chain L) in PDB entry 1NSK
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 PRO 59 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57L ASP 4.5 2.2 - - - +
58L ARG* 1.3 90.4 - - + +
60L PHE* 1.3 67.6 + - + +
62L PRO* 3.2 15.2 - - - +
63L GLY 5.2 0.2 + - - -
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Residues in contact with PHE 60 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55L LEU* 3.6 42.0 - - + -
58L ARG* 4.1 21.1 - - + -
59L PRO* 1.3 81.9 - - + +
61L PHE* 1.3 83.0 + - - +
63L GLY* 2.8 17.8 + - - -
64L LEU* 2.9 31.2 + - + +
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Residues in contact with PHE 61 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49L LYS* 3.6 31.9 - - + -
52L TYR* 3.3 39.9 - - + -
55L LEU* 3.1 31.4 - - + +
56L LYS* 3.6 25.8 - - + +
58L ARG 2.9 11.7 + - - +
60L PHE* 1.3 83.6 - - - +
62L PRO* 1.3 74.0 - - + +
64L LEU* 3.1 5.8 + - + +
65L VAL* 3.0 48.8 + - + +
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Residues in contact with PRO 62 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58L ARG 4.0 1.6 - - - +
59L PRO* 3.2 17.9 - - + +
60L PHE 3.5 0.9 - - - -
61L PHE* 1.3 102.6 - - + +
63L GLY* 1.3 62.2 + - - +
65L VAL* 3.3 5.8 + - + +
66L LYS* 3.1 21.5 + - - +
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Residues in contact with GLY 63 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60L PHE 2.8 13.6 + - - -
62L PRO* 1.3 74.8 - - - +
64L LEU* 1.3 50.2 + - - -
66L LYS* 2.9 10.0 + - - +
67L TYR* 2.7 42.2 + - - +
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Residues in contact with LEU 64 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12L LYS* 5.8 3.6 - - - +
52L TYR* 3.6 59.0 - - + +
55L LEU* 4.2 4.3 - - + -
60L PHE* 2.9 42.2 + - + +
61L PHE* 3.4 12.6 - - + +
63L GLY* 1.3 75.1 - - - +
65L VAL* 1.3 56.3 + - - +
67L TYR* 3.1 12.4 - - + +
68L MET* 3.0 38.7 + - + +
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Residues in contact with VAL 65 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45L GLU* 3.5 46.2 - - + +
48L LEU* 3.6 14.2 - - + +
49L LYS* 4.0 15.5 - - + +
52L TYR* 4.9 3.8 - - + -
61L PHE* 3.0 49.7 + - + +
62L PRO* 3.7 7.4 - - + +
64L LEU* 1.3 75.5 - - - +
66L LYS* 1.3 66.0 + - - +
67L TYR 3.2 0.7 + - - -
68L MET 3.5 0.3 + - - -
69L ASN* 3.3 22.2 + - - +
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Residues in contact with LYS 66 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45L GLU* 4.5 17.5 + - - +
62L PRO 3.1 13.1 + - - +
63L GLY* 2.9 11.8 + - - +
65L VAL* 1.3 76.1 - - - +
67L TYR* 1.3 64.6 + - - +
69L ASN* 3.5 8.1 + - - +
70L SER* 3.3 18.5 + - - -
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Residues in contact with TYR 67 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12L LYS* 6.3 2.7 - - + -
13L PRO* 4.0 6.8 - - + +
14L ASP* 4.9 8.7 - - + -
63L GLY 2.7 19.9 + - - +
64L LEU* 3.1 20.2 - - + +
66L LYS* 1.3 70.9 - - - +
68L MET* 1.3 65.3 + - + +
69L ASN 3.0 3.4 - - - -
70L SER* 2.6 40.1 + - - -
111L GLN* 5.1 0.2 + - - -
113L GLY* 2.6 39.8 + - - -
114L ARG* 2.5 64.6 + - - +
149N TRP* 5.6 1.1 - + - -
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Residues in contact with MET 68 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10L ALA* 5.5 8.7 - - + -
12L LYS* 3.6 39.0 - - + -
13L PRO* 3.8 18.6 - - - +
43L ALA* 4.0 5.2 + - - +
48L LEU* 3.5 37.6 - - + +
51L HIS* 6.0 2.0 - - + -
52L TYR* 3.5 32.5 - - + +
64L LEU* 3.0 19.8 + - + +
65L VAL 3.5 0.2 + - - -
67L TYR* 1.3 83.5 - - + +
69L ASN* 1.3 57.1 + - - +
71L GLY 3.8 10.9 - - - +
73L VAL* 4.2 20.5 - - + +
118L HIS* 5.6 2.0 - - + -
133L TRP* 5.4 8.1 - - + -
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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