Contacts of the strand formed by residues 100 - 110 (chain C) in PDB entry 6NQN
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 ILE 100 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A SER* 3.7 31.4 - - - +
100A ILE* 4.6 6.7 - - + -
102A ASN* 3.3 15.7 + - - +
92C SER* 3.7 22.7 - - - +
93C MET 3.4 7.9 - - - +
94C ASN* 3.1 38.4 - - + +
98C GLY* 3.1 24.5 - - - +
99C GLY* 1.3 75.5 - - - +
101C CYS* 1.3 64.7 + - - +
102C ASN* 4.4 1.1 - - - +
122C GLY* 3.2 1.2 - - - -
123C VAL* 2.8 32.4 + - + +
125C PHE* 4.2 0.8 - - - -
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Residues in contact with CYS 101 (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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56C ILE* 4.2 4.0 - - - -
92C SER* 3.4 2.8 - - - -
93C MET* 2.7 57.6 + - + +
95C TYR* 4.1 7.4 - - + -
100C ILE* 1.3 72.7 - - - +
102C ASN* 1.3 62.1 + - - +
120C PHE* 3.4 35.2 - - + -
121C ASP 3.4 4.7 - - - +
122C GLY* 3.7 6.7 - - - -
125C PHE* 3.4 36.1 - - - -
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Residues in contact with ASN 102 (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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100A ILE* 3.2 25.1 + - - +
102A ASN* 3.4 26.3 + - + +
121A ASP* 3.2 32.1 + - + +
123A VAL* 3.6 19.8 - - + +
91C ARG 3.4 2.5 - - - -
92C SER* 3.0 26.5 + - - -
93C MET* 4.7 0.2 - - - -
100C ILE* 4.4 0.3 - - - +
101C CYS* 1.3 72.2 - - - +
103C ALA* 1.3 62.8 + - - +
119C ARG* 4.1 0.3 - - - +
120C PHE* 3.5 1.0 - - - -
121C ASP* 2.8 38.0 + - - +
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Residues in contact with ALA 103 (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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123A VAL* 4.1 1.5 - - - +
60C VAL* 3.9 35.4 - - + -
89C TRP* 3.7 8.5 - - + -
90C GLU* 3.4 0.2 - - - -
91C ARG 2.8 34.4 + - - +
93C MET* 3.9 9.6 - - + -
102C ASN* 1.3 76.5 - - - +
104C THR* 1.3 67.6 + - - +
119C ARG 3.2 11.7 - - - +
120C PHE* 4.1 5.4 - - + -
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Residues in contact with THR 104 (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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17A ALA* 6.3 1.3 - - + -
20A GLY* 4.1 31.0 + - - +
122A GLY 5.5 0.2 - - - +
123A VAL* 3.8 21.5 - - + -
89C TRP* 3.3 11.2 - - - -
90C GLU* 4.2 9.2 - - + -
103C ALA* 1.3 79.5 - - - +
105C ASN* 1.3 63.5 + - - +
117C GLU 4.4 1.3 + - - -
118C ILE* 3.3 8.4 - - - +
119C ARG* 3.0 48.3 + - + +
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Residues in contact with ASN 105 (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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60C VAL 4.2 1.6 + - - -
63C KZ4 3.2 22.6 + - - -
88C SER* 3.2 5.6 - - - -
89C TRP* 2.9 59.8 + - + +
104C THR* 1.3 75.4 - - - +
106C ASP* 1.3 63.6 + - - +
107C ILE* 3.5 14.5 + - - +
116C TYR* 3.2 41.8 - - - +
117C GLU 3.5 3.0 - - - +
118C ILE* 3.5 16.5 - - + +
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Residues in contact with ASP 106 (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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88C SER* 3.7 10.9 - - - -
104C THR 4.4 0.2 - - - -
105C ASN* 1.3 73.6 + - - +
107C ILE* 1.3 61.0 + - - +
108C THR* 4.0 17.3 + - - +
115C ILE 3.3 4.2 - - - +
117C GLU* 3.1 49.3 + - - +
180C LYS* 2.7 31.4 + - - -
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Residues in contact with ILE 107 (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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63C KZ4 3.7 20.0 - - - +
65C ASN* 3.7 13.9 - - + +
83C PHE* 3.9 21.1 - - + -
86C GLY* 3.6 3.8 - - - -
87C TYR* 3.0 67.8 + - + +
89C TRP* 4.1 3.8 - - + +
105C ASN* 3.5 26.2 - - - +
106C ASP* 1.3 70.8 - - - +
108C THR* 1.3 75.6 + - - +
114C TYR* 4.3 2.9 - - + -
115C ILE 3.3 2.2 - - - -
116C TYR* 3.7 19.7 - - + -
180C LYS* 3.8 3.1 - - - -
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Residues in contact with THR 108 (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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83C PHE* 4.5 2.7 - - - -
85C GLU 4.7 9.2 - - - +
106C ASP* 4.0 18.3 + - - +
107C ILE* 1.3 83.4 - - - +
109C LEU* 1.3 64.4 + - - +
114C TYR* 3.4 5.5 - - - -
115C ILE* 2.8 48.7 + - - +
180C LYS* 4.5 9.4 - - - -
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Residues in contact with LEU 109 (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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4C ILE* 5.5 7.9 - - + +
8C MET* 3.6 27.4 - - + -
83C PHE* 3.8 25.4 - - + -
84C PRO* 3.8 38.7 + - + +
108C THR* 1.3 78.1 - - - +
110C ASP* 1.3 60.3 + - - +
111C GLY 3.5 25.9 + - - +
113C CYS 3.5 20.2 - - - +
114C TYR* 3.9 8.3 - - + -
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Residues in contact with ASP 110 (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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11C LYS* 5.3 6.4 + - - -
108C THR 4.3 0.2 - - - -
109C LEU* 1.3 73.8 - - - +
111C GLY* 1.3 62.7 + - - +
112C ASP* 3.1 1.0 + - - +
113C CYS* 2.8 38.2 + - + +
115C ILE* 4.3 17.0 - - + +
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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