Contacts of the helix formed by residues 92 - 107 (chain F) in PDB entry 2NPP
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 TYR 92 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107E GLU* 5.3 4.9 + - - -
20F CYS* 3.6 25.1 - - - -
60F GLY 3.1 9.9 + - - +
62F PHE* 3.6 25.6 - - + -
63F HIS* 3.7 26.4 - + - -
91F TYR* 1.3 121.1 - + + +
93F SER* 1.3 59.9 + - - +
94F VAL 3.2 2.9 + - - -
95F GLU* 3.5 21.8 + - - +
96F THR* 2.5 30.0 + - - -
132F GLU* 3.4 1.6 - - - -
136F LYS* 4.3 2.7 - - - -
267F TYR* 4.3 8.5 - - - -
294F ARG* 4.9 6.7 + - - -
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Residues in contact with SER 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60F GLY* 3.6 14.7 + - - -
86F TYR 5.0 0.2 - - - +
87F VAL* 4.0 4.7 - - - +
88F ASP* 3.4 27.1 + - - -
90F GLY 4.1 7.6 + - - -
92F TYR* 1.3 75.5 - - - +
94F VAL* 1.3 66.0 + - - +
96F THR* 3.1 1.4 + - - -
97F VAL* 2.8 27.3 + - - +
129F PHE* 3.4 29.2 + - - -
132F GLU* 2.9 16.5 + - - -
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Residues in contact with VAL 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F GLN* 4.3 11.4 - - + -
93F SER* 1.3 72.2 - - - +
95F GLU* 1.3 72.4 + - - +
97F VAL* 3.0 7.5 - - - +
98F THR* 2.7 38.1 + - - +
129F PHE* 4.1 2.9 - - + -
132F GLU* 2.5 40.3 + - + +
133F CYS* 4.0 28.0 - - - -
136F LYS* 3.9 9.2 - - + -
137F TYR* 3.8 28.7 - - + +
146F PHE* 5.2 5.4 - - + -
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Residues in contact with GLU 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F LEU* 4.6 8.2 - - + +
20F CYS* 3.8 36.4 - - - +
21F LYS 4.6 0.7 - - - -
22F GLN* 4.2 19.8 + - - +
62F PHE* 3.9 22.2 - - + -
92F TYR* 3.5 20.2 - - + +
94F VAL* 1.3 77.5 - - - +
96F THR* 1.3 65.1 + - - +
98F THR* 3.6 4.9 - - - -
99F LEU* 2.8 27.8 + - - +
136F LYS* 2.9 36.2 + - - +
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Residues in contact with THR 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58F VAL* 3.8 28.9 - - + -
60F GLY* 3.3 24.3 + - - -
62F PHE* 3.5 19.2 + - - -
65F LEU* 4.2 13.0 - - + +
86F TYR 4.1 7.4 - - - +
92F TYR 2.5 19.5 + - - -
93F SER 3.2 7.4 - - - -
95F GLU* 1.3 80.0 - - - +
97F VAL* 1.3 64.7 + - - +
99F LEU* 3.4 2.8 + - - +
100F LEU* 3.1 30.6 + - + +
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Residues in contact with VAL 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86F TYR* 4.4 19.9 - - + +
87F VAL* 4.0 12.8 - - + -
93F SER 2.8 17.6 + - - +
94F VAL* 3.0 17.5 - - - +
96F THR* 1.3 73.8 - - - +
98F THR* 1.3 62.8 + - - +
100F LEU* 3.2 5.2 + - - +
101F VAL* 2.8 42.2 + - + +
129F PHE* 4.1 15.0 - - + -
146F PHE* 4.0 31.2 - - + -
150F PHE* 4.2 17.3 - - + -
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Residues in contact with THR 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F LEU* 3.3 23.8 - - + -
23F LEU* 3.7 30.1 + - + +
28F VAL* 5.3 3.7 - - + +
31F LEU* 3.8 11.5 - - + +
94F VAL* 2.7 31.7 + - - +
95F GLU* 3.6 3.4 - - - -
97F VAL* 1.3 76.8 - - - +
99F LEU* 1.3 53.0 + - - +
101F VAL* 3.3 2.1 + - - +
102F ALA* 2.7 36.6 + - - +
137F TYR* 5.2 1.6 + - - -
146F PHE* 3.4 25.0 - - + -
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Residues in contact with LEU 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14F ILE* 4.0 20.6 - - + -
17F LEU* 3.2 26.4 - - + +
18F ASN* 4.5 11.2 - - - +
62F PHE* 3.9 11.0 - - + -
65F LEU* 4.1 11.9 - - + -
66F MET* 3.4 34.1 - - + -
69F PHE* 4.8 4.5 - - + -
95F GLU 2.8 21.7 + - - +
96F THR 3.7 2.5 - - - +
98F THR* 1.3 72.5 - - - +
100F LEU* 1.3 65.7 + - + +
102F ALA* 3.1 1.7 + - + +
103F LEU* 2.9 41.8 + - + +
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Residues in contact with LEU 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58F VAL* 5.0 4.0 - - + -
65F LEU* 4.4 15.7 - - + -
69F PHE* 4.5 8.3 - - + -
82F PHE* 3.6 43.7 - - + -
86F TYR* 3.7 36.1 - - + -
96F THR* 3.1 25.4 + - + +
97F VAL* 3.6 7.2 - - - +
99F LEU* 1.3 75.9 - - + +
101F VAL* 1.3 64.8 + - + +
103F LEU* 3.1 20.5 + - + +
104F LYS* 3.2 10.4 + - - +
111F ILE* 3.7 7.0 - - + +
113F ILE* 4.7 13.6 - - + +
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Residues in contact with VAL 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F LEU* 3.9 23.3 - - + +
32F CYS* 5.3 0.2 - - - -
35F ALA* 4.0 13.0 - - + -
86F TYR* 6.2 2.5 - - + -
97F VAL* 2.8 36.9 + - + +
98F THR* 3.7 4.3 - - - +
100F LEU* 1.3 74.2 - - + +
102F ALA* 1.3 63.2 + - - +
104F LYS* 3.0 17.8 + - + +
105F VAL* 3.0 12.6 + - - +
113F ILE* 4.4 16.2 - - + -
146F PHE* 4.5 5.4 - - + -
149F LEU* 3.8 33.7 - - + -
150F PHE* 5.9 1.1 - - + -
153F LEU* 6.2 0.9 - - + -
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Residues in contact with ALA 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F LEU* 3.5 12.1 - - + +
13F TRP* 5.4 2.5 - - + -
14F ILE* 3.8 21.5 - - + +
17F LEU* 4.1 13.5 - - + -
31F LEU* 3.8 18.8 - - + -
98F THR 2.7 21.2 + - - +
99F LEU* 3.1 7.4 + - - +
101F VAL* 1.3 73.6 - - - +
103F LEU* 1.3 63.1 + - - +
105F VAL* 3.5 0.7 + - - +
106F ARG* 3.1 23.0 + - - +
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Residues in contact with LEU 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F ILE* 3.5 32.8 - - + -
69F PHE* 4.5 18.2 - - + -
75F SER* 4.2 24.2 - - - +
82F PHE* 6.3 0.2 - - + -
99F LEU* 2.9 33.8 + - + +
100F LEU* 3.5 8.3 - - + +
102F ALA* 1.3 75.4 - - - +
104F LYS* 1.3 58.9 + - - +
106F ARG* 4.2 1.3 - - - -
107F TYR* 2.8 51.6 + - + +
111F ILE* 3.0 24.5 - - + -
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Residues in contact with LYS 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F ALA* 6.5 1.6 - - + -
38F ILE* 4.5 17.7 - - + +
39F LEU* 4.5 15.5 - - + -
42F GLU* 3.0 37.7 + - - -
100F LEU 3.2 6.6 + - - +
101F VAL* 3.0 9.9 + - + +
103F LEU* 1.3 77.0 - - - +
105F VAL* 1.3 64.8 - - + +
106F ARG 3.2 0.2 + - - -
107F TYR 4.4 0.2 - - - -
108F ARG* 3.1 42.8 + - - +
111F ILE* 3.1 41.6 + - + +
112F THR* 4.0 12.5 + - - +
113F ILE* 4.1 28.2 - - + +
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Residues in contact with VAL 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F PHE* 4.5 2.9 - - + -
10F LEU* 3.4 21.4 - - + +
31F LEU* 3.5 33.0 - - + +
34F LYS* 4.2 26.6 + - + +
35F ALA* 4.0 19.5 - - + -
38F ILE* 3.8 25.1 - - + +
101F VAL* 3.0 13.8 + - + +
102F ALA 3.8 6.1 - - - +
104F LYS* 1.3 78.7 - - + +
106F ARG* 1.3 64.4 + - - +
108F ARG* 4.3 8.3 + - - +
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Residues in contact with ARG 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574D ASP* 4.2 7.6 + - - +
577D TYR* 3.0 41.8 + - - -
578D PHE* 4.9 0.6 - - - -
7F THR* 4.1 20.0 + - - +
10F LEU* 3.5 25.1 - - + +
11F ASP* 3.2 27.5 + - - -
14F ILE* 3.8 13.9 - - + -
102F ALA 3.1 17.9 + - - +
103F LEU 3.5 2.2 - - - +
104F LYS 3.1 0.8 - - - -
105F VAL* 1.3 80.7 - - - +
107F TYR* 1.3 108.6 + - + +
108F ARG* 2.9 10.2 + - - +
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Residues in contact with TYR 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574D ASP* 3.8 15.0 - - - -
578D PHE* 4.3 12.1 - + - -
11F ASP* 3.7 15.1 + - - -
14F ILE* 4.9 3.1 - - + -
75F SER* 3.8 15.7 - - - +
76F PRO* 3.3 45.3 - - + +
103F LEU* 2.8 27.3 + - + +
106F ARG* 1.3 119.0 + - + +
108F ARG* 1.3 62.9 + - - +
109F GLU 3.2 3.4 - - - -
110F ARG* 3.1 30.4 + - + -
111F ILE* 3.6 12.5 + - + +
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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
------------------------------------------------------------
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