Contacts of the strand formed by residues 74 - 79 (chain C) in PDB entry 1NYU
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 74 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C TYR* 6.3 0.2 - - + -
32C TYR* 3.3 15.3 - - - +
33C ASN* 3.8 28.3 - - - +
35C ASN* 5.3 7.2 - - - -
60C TYR* 3.6 14.2 - - + +
61C ALA 3.5 0.7 - - - -
62C SER* 2.6 46.0 + - - +
72C LEU 3.5 1.0 - - - -
73C VAL* 1.3 90.4 - - + +
75C LYS* 1.3 61.1 + - - +
92D LEU* 5.1 4.7 - - + -
100D ILE* 3.0 39.4 + - + -
101D ILE* 3.0 21.8 - - - +
102D LYS* 3.6 18.2 - - + +
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Residues in contact with LYS 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C ILE* 3.7 25.3 - - + +
31C TYR* 3.3 14.9 - - - -
32C TYR* 3.0 25.1 + - + +
60C TYR* 3.4 16.9 + - - +
61C ALA* 3.3 24.0 - - + -
72C LEU* 3.4 39.7 - - + +
74C LYS* 1.3 74.8 - - - +
76C GLY* 1.3 59.0 + - - +
110C ASN* 3.1 19.9 + - - +
111C GLU* 2.7 42.4 + - - +
113C PHE* 3.7 10.8 - - - -
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Residues in contact with GLY 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C CYS* 5.0 1.6 - - - -
30C ILE 3.6 12.2 + - - -
31C TYR* 4.4 1.1 - - - -
47C GLU* 3.1 13.9 - - - -
59C CYS* 3.4 3.6 - - - +
60C TYR* 2.6 53.6 + - - +
75C LYS* 1.3 76.0 - - - +
77C CYS* 1.3 60.0 + - - -
110C ASN* 4.3 0.2 + - - -
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Residues in contact with CYS 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C CYS* 4.7 0.9 - - - -
47C GLU* 2.8 48.4 + - - +
48C ARG 4.2 0.2 - - - -
49C CYS* 2.0 55.6 - - + -
57C LEU* 6.2 0.4 - - + -
58C HIS 3.7 4.9 - - - +
59C CYS* 4.0 2.2 - - - +
60C TYR* 2.9 17.2 - - - -
76C GLY* 1.3 72.8 - - - -
78C TRP* 1.3 59.2 + - - +
104D ASP* 4.1 13.2 - - - +
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Residues in contact with TRP 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C LEU* 4.4 1.6 - - - +
58C HIS* 2.4 64.7 + + + +
59C CYS 4.0 7.6 - - - +
60C TYR* 3.3 38.8 - + + -
77C CYS* 1.3 69.7 - - - +
79C LEU* 1.3 90.1 + - - +
80C ASP 5.1 1.4 + - - -
83C ASN* 6.0 2.7 - - + +
84C CYS* 5.1 0.2 - - + -
101C PHE* 3.5 36.3 - + - -
103C CYS* 3.9 18.9 - - - -
31D ALA* 3.2 26.5 - - + -
32D PRO* 3.8 14.7 - - + +
90D SER* 3.3 39.9 - - - +
91D MET 4.1 1.1 - - - -
92D LEU* 4.2 13.2 - - + -
104D ASP* 5.1 0.4 - - - -
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Residues in contact with LEU 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C GLU 5.3 6.1 - - - +
51C GLY* 5.8 1.6 - - - -
52C GLU* 5.6 8.5 - - + +
56C ARG 5.3 0.2 - - - -
57C LEU* 4.3 19.3 - - + -
58C HIS* 3.4 2.1 - - - +
77C CYS 4.4 0.2 - - - -
78C TRP* 1.3 97.1 + - - +
80C ASP* 1.3 75.7 + - + +
88D PRO* 4.0 41.1 - - + +
89D MET* 4.1 6.1 - - - +
90D SER* 4.1 17.1 + - - +
104D ASP* 4.2 25.8 + - + -
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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