Contacts of the helix formed by residues 96 - 114 (chain D) in PDB entry 2NP5
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 ASP 96 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94D PRO 3.4 0.8 - - - -
95D LEU* 1.3 79.6 - - - +
97D GLU* 1.3 53.9 + - - +
98D ALA* 3.3 8.4 + - - +
99D ARG* 2.9 51.3 + - - +
100D SER* 2.7 38.2 + - - -
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Residues in contact with GLU 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D ASP* 1.3 74.8 - - - +
98D ALA* 1.3 62.0 + - - +
100D SER* 3.1 9.3 + - - -
101D ARG* 3.1 65.1 + - - +
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Residues in contact with ALA 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D ASP* 3.3 8.9 + - - +
97D GLU* 1.3 78.8 - - - +
99D ARG* 1.3 59.7 + - + +
101D ARG* 3.5 23.0 + - - +
102D GLU* 3.1 38.0 + - - +
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Residues in contact with ARG 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D SER* 3.1 33.9 + - - -
91D GLN* 3.5 49.1 + - - +
92D LEU 5.6 0.3 - - - -
93D LEU 3.4 13.0 - - - +
94D PRO* 4.0 2.8 - - - +
95D LEU* 3.7 28.2 + - - +
96D ASP* 2.9 40.1 + - - +
98D ALA* 1.3 76.8 - - + +
100D SER* 1.3 60.7 + - - +
102D GLU* 3.9 13.7 - - - +
103D ALA* 2.9 29.5 + - - +
177D GLU* 5.5 1.8 + - - -
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Residues in contact with SER 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D PRO* 3.6 23.4 - - - +
96D ASP 2.7 24.3 + - - -
97D GLU* 3.1 14.5 + - - -
99D ARG* 1.3 73.4 - - - +
101D ARG* 1.3 57.2 + - - +
103D ALA* 3.4 2.8 + - - +
104D HIS* 3.0 26.3 + - - +
165D ILE* 5.0 3.1 - - - +
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Residues in contact with ARG 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D PHE* 4.6 7.4 - - + +
20D ASP* 4.5 22.3 + - - +
23D ALA* 3.2 28.5 - - + -
97D GLU* 3.1 51.3 + - - +
98D ALA* 3.6 21.0 - - - +
100D SER* 1.3 73.7 - - - +
102D GLU* 1.3 66.2 + - - +
104D HIS* 3.6 6.4 - - + +
105D VAL* 3.0 28.5 + - - +
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Residues in contact with GLU 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D ALA* 5.8 3.3 - - - +
19D PHE* 3.7 45.1 - - + +
64D LEU* 4.3 19.2 - - + +
91D GLN* 4.4 12.0 - - - +
98D ALA* 3.1 30.0 + - - +
99D ARG* 3.9 11.2 - - - +
100D SER 3.4 0.2 - - - -
101D ARG* 1.3 76.4 - - - +
103D ALA* 1.3 57.6 + - - +
105D VAL* 3.2 2.3 + - - +
106D MSE 2.8 38.3 + - + +
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Residues in contact with ALA 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D LEU* 4.1 20.2 - - - +
94D PRO* 4.2 14.4 - - + -
99D ARG 2.9 19.0 + - - +
100D SER 3.7 4.3 - - - +
102D GLU* 1.3 76.0 - - - +
104D HIS* 1.3 57.0 + - - +
106D MSE 3.8 6.4 - - - +
107D ALA* 2.9 26.5 + - - +
161D ALA* 4.3 7.5 - - + +
165D ILE* 3.2 21.2 - - + +
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Residues in contact with HIS 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B VAL* 4.0 25.0 + - + +
114B ALA* 4.0 29.5 - - + +
115B THR* 4.0 19.5 - - + +
23D ALA* 4.2 22.7 + - + +
100D SER 3.0 17.4 + - - +
101D ARG* 3.6 9.4 - - + +
103D ALA* 1.3 75.3 - - - +
105D VAL* 1.3 62.8 + - + +
107D ALA* 3.5 1.2 + - - +
108D ALA* 3.0 22.4 + - + +
165D ILE* 3.5 14.9 - - + +
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Residues in contact with VAL 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D LEU* 6.2 0.2 - - + -
19D PHE* 3.5 32.3 - - + +
22D ALA* 3.6 13.7 - - + +
23D ALA* 3.3 33.4 - - - +
27D LEU* 3.9 19.4 - - + +
57D PHE* 4.2 11.7 - - + -
61D LEU* 6.2 0.4 - - + -
101D ARG 3.0 21.1 + - - +
102D GLU 3.7 3.1 - - - +
104D HIS* 1.3 76.7 - - - +
106D MSE 1.3 58.2 + - - +
108D ALA* 3.2 8.2 + - - +
109D PHE* 2.9 28.1 + - + +
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Residues in contact with MSE 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D PHE* 4.2 9.2 - - + -
61D LEU* 3.1 42.2 - - + -
64D LEU* 3.6 30.5 - - + -
92D LEU* 5.3 8.5 - - + -
102D GLU* 2.8 28.3 + - + +
103D ALA* 3.8 6.5 - - - +
105D VAL* 1.3 73.6 - - - +
107D ALA* 1.3 57.9 + - - +
109D PHE* 3.3 7.7 + - + +
110D ALA* 3.0 26.5 + - - +
123D ARG* 4.2 26.1 + - - +
126D THR* 4.7 11.4 - - + -
130D ILE* 6.1 1.8 - - + -
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Residues in contact with ALA 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B VAL* 3.8 19.3 - - + -
162B LEU* 4.6 7.3 - - + +
103D ALA 2.9 17.2 + - - +
104D HIS 3.8 2.9 - - - +
106D MSE 1.3 74.1 - - - +
108D ALA* 1.3 64.4 + - - +
110D ALA* 3.1 8.3 + - - +
111D VAL* 2.9 26.7 + - - +
161D ALA* 6.5 0.2 - - + -
162D LEU* 3.9 19.1 - - + +
165D ILE* 3.9 12.1 - - + -
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Residues in contact with ALA 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B GLU* 4.2 8.1 - - - +
111B VAL* 4.1 21.4 - - + +
27D LEU* 3.5 23.4 - - + +
104D HIS* 3.0 17.9 + - + +
105D VAL* 3.5 9.6 - - - +
107D ALA* 1.3 74.7 - - - +
109D PHE* 1.3 57.1 + - - +
111D VAL* 3.3 5.5 + - - +
112D ARG* 2.8 29.5 + - - +
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Residues in contact with PHE 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D LEU* 3.6 10.0 - - + +
57D PHE* 4.0 41.7 - + + -
61D LEU* 3.5 27.1 - - + -
105D VAL* 2.9 16.0 + - + +
106D MSE 3.5 15.5 - - - +
108D ALA* 1.3 73.9 - - - +
110D ALA* 1.3 55.1 + - - +
112D ARG* 3.2 3.1 + - - +
113D ALA* 2.8 34.1 + - - +
119D LEU* 3.5 60.1 - - + +
122D ILE* 3.8 17.7 - - + -
123D ARG* 3.8 22.2 - - + -
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Residues in contact with ALA 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B LEU* 3.7 29.1 - - + +
165B ILE* 4.6 9.2 - - - +
166B GLY* 4.6 2.1 - - - -
106D MSE 3.0 11.4 + - - +
107D ALA* 3.5 7.9 - - - +
109D PHE* 1.3 77.4 - - - +
111D VAL* 1.3 63.1 + - - +
113D ALA* 3.3 14.2 - - - +
114D ALA 3.7 3.3 + - - -
123D ARG* 3.2 40.4 - - - +
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Residues in contact with VAL 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B GLY* 5.9 1.8 - - - -
27B LEU 5.8 2.0 - - - +
28B GLU* 4.2 14.6 - - + +
104B HIS* 4.2 14.1 + - + +
107B ALA* 3.7 28.0 - - + +
108B ALA* 3.9 24.5 - - + +
111B VAL* 3.6 21.5 - - + -
162B LEU* 4.4 4.0 - - + -
165B ILE* 4.7 5.6 - - - -
107D ALA 2.9 17.3 + - - +
108D ALA* 3.6 8.7 - - - +
110D ALA* 1.3 72.9 - - - +
112D ARG* 1.3 65.5 + - - +
114D ALA* 3.0 22.3 + - - +
115D THR* 4.2 1.9 + - - -
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Residues in contact with ARG 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B SER 5.8 0.4 + - - -
28B GLU* 3.8 24.1 + - - +
27D LEU* 4.2 15.9 - - + -
108D ALA 2.8 20.7 + - - +
109D PHE 3.5 5.2 - - - +
111D VAL* 1.3 73.2 - - - +
113D ALA* 1.3 62.2 + - - +
115D THR* 2.8 49.7 + - - -
116D SER* 3.1 27.1 + - - -
119D LEU* 3.3 25.7 - - + +
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Residues in contact with ALA 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B GLY* 3.9 15.3 - - - +
109D PHE* 2.8 15.8 + - + +
110D ALA* 3.3 15.9 - - - +
111D VAL 3.2 0.4 - - - -
112D ARG* 1.3 73.0 - - - +
114D ALA* 1.3 61.6 + - - +
115D THR 3.2 0.7 + - - -
116D SER 3.5 15.2 + - - +
119D LEU* 4.2 7.4 - - - +
120D ALA* 3.5 38.8 - - - +
123D ARG* 4.5 7.6 - - + -
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Residues in contact with ALA 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B HIS* 3.6 31.1 - - + +
165B ILE* 3.5 33.7 + - + +
110D ALA 3.7 2.0 + - - -
111D VAL 3.0 16.7 + - - +
113D ALA* 1.3 78.3 - - - +
115D THR* 1.3 60.6 + - - +
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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