Contacts of the helix formed by residues 96 - 114 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A PRO 3.3 0.6 - - - -
95A LEU* 1.3 79.2 - - - +
97A GLU* 1.3 66.3 + - - +
98A ALA* 3.5 9.0 + - - +
99A ARG* 2.9 64.6 + - - +
100A SER* 2.9 26.2 + - - -
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Residues in contact with GLU 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A ASP* 1.3 75.4 - - - +
98A ALA* 1.3 63.3 + - - +
100A SER* 3.2 14.6 + - - -
101A ARG* 3.0 40.1 + - + +
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Residues in contact with ALA 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A PHE* 5.0 0.5 - - - -
96A ASP* 3.3 10.3 + - - +
97A GLU* 1.3 78.2 - - - +
99A ARG* 1.3 62.2 + - + +
101A ARG* 3.3 11.6 + - - +
102A GLU* 3.1 35.8 + - - +
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Residues in contact with ARG 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ARG* 3.8 9.4 - - - +
90A SER* 3.0 25.0 + - - -
91A GLN* 3.7 35.0 - - - +
92A LEU 5.9 0.2 - - - -
93A LEU 3.2 23.8 + - - +
94A PRO* 3.8 7.1 - - + +
95A LEU* 3.6 26.8 - - - +
96A ASP* 2.9 42.8 + - - +
98A ALA* 1.3 74.7 - - + +
100A SER* 1.3 59.7 + - - +
102A GLU* 3.5 22.5 - - - +
103A ALA* 2.9 29.3 + - - +
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Residues in contact with SER 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A PRO* 3.6 25.9 + - - +
96A ASP 2.9 20.0 + - - -
97A GLU* 3.2 18.0 + - - -
99A ARG* 1.3 72.7 - - - +
101A ARG* 1.3 66.1 + - - +
103A ALA* 3.3 3.0 + - - +
104A HIS* 3.1 23.4 + - - +
165A ILE* 5.8 0.3 - - - +
168A PRO* 5.7 6.7 - - - +
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Residues in contact with ARG 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A PHE* 3.4 39.9 - - + -
20A ASP* 2.6 42.8 + - - +
23A ALA* 4.0 19.5 - - + +
24A GLU* 5.5 2.6 - - - +
97A GLU* 3.0 41.2 + - - +
98A ALA* 3.6 11.0 - - - +
100A SER* 1.3 76.6 - - - +
102A GLU* 1.3 61.2 + - - +
104A HIS* 3.3 6.2 + - - +
105A VAL* 3.1 28.2 + - - +
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Residues in contact with GLU 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A PHE* 3.7 15.9 - - + -
64A LEU* 4.0 21.4 - - + +
67A LYS* 5.4 3.6 - - - +
68A LEU* 3.4 15.6 - - + +
71A ARG* 2.8 45.1 + - - -
91A GLN 4.4 0.7 - - - +
98A ALA* 3.1 23.9 + - - +
99A ARG* 3.5 17.1 - - - +
101A ARG* 1.3 76.9 - - - +
103A ALA* 1.3 58.1 + - - +
105A VAL* 3.4 1.0 + - - +
106A MSE 2.8 36.8 + - + +
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Residues in contact with ALA 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A LEU 5.8 1.3 - - - +
93A LEU 5.8 0.2 - - - -
94A PRO* 4.1 18.6 - - + -
99A ARG 2.9 18.5 + - - +
100A SER 3.5 5.6 - - - +
102A GLU* 1.3 75.7 - - - +
104A HIS* 1.3 57.5 + - - +
106A MSE 4.0 3.8 - - - +
107A ALA* 2.9 33.6 + - - +
161A ALA* 4.2 27.0 - - + +
165A ILE* 4.0 5.2 - - + +
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Residues in contact with HIS 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ALA 3.4 22.6 + - - -
23A ALA 3.1 23.0 + - - -
26A GLY* 4.0 17.4 - - - -
100A SER 3.1 13.2 + - - +
101A ARG* 3.6 10.3 - - - +
102A GLU 3.3 0.2 - - - -
103A ALA* 1.3 76.6 - - - +
105A VAL* 1.3 65.6 + - + +
107A ALA* 3.8 2.3 - - - +
108A ALA* 3.0 20.3 + - + +
165A ILE* 3.9 16.5 - - + +
111C VAL* 4.2 17.5 + - + +
114C ALA* 3.3 34.6 - - + +
115C THR* 4.4 8.4 - - + +
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Residues in contact with VAL 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LEU* 5.4 0.7 - - + -
19A PHE* 3.8 36.3 - - + +
22A ALA* 3.9 18.6 - - + -
23A ALA* 3.6 33.4 - - + +
27A LEU* 5.1 1.1 - - + -
64A LEU* 3.9 3.8 - - + -
101A ARG 3.1 17.0 + - - +
102A GLU 4.0 0.4 - - - +
104A HIS* 1.3 77.9 - - - +
106A MSE 1.3 62.6 + - - +
108A ALA* 3.2 7.5 + - - +
109A PHE* 3.0 46.5 + - + -
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Residues in contact with MSE 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A LEU* 3.7 27.1 - - + -
64A LEU* 3.5 28.5 - - + -
65A VAL* 4.0 11.9 - - + -
68A LEU* 3.9 27.6 - - + -
102A GLU 2.8 26.6 + - - +
103A ALA* 4.0 4.5 - - - +
105A VAL* 1.3 71.8 - - - +
107A ALA* 1.3 58.4 + - - +
109A PHE* 3.2 4.8 + - + -
110A ALA* 2.9 27.0 + - - +
123A ARG* 4.3 27.8 - - - +
126A THR* 6.2 0.9 - - + -
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Residues in contact with ALA 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A ALA 2.9 19.2 + - - +
104A HIS 3.8 0.7 - - - +
106A MSE 1.3 76.6 - - - +
108A ALA* 1.3 59.6 + - - +
110A ALA* 3.2 8.0 + - - +
111A VAL* 3.0 27.2 + - - +
161A ALA* 6.2 0.4 - - + -
162A LEU* 4.1 12.3 - - + +
165A ILE* 3.5 24.5 - - + -
111C VAL* 3.8 12.1 - - + -
162C LEU* 4.6 8.7 - - + +
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Residues in contact with ALA 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ALA* 5.9 1.3 - - + +
26A GLY* 5.4 0.4 - - - -
27A LEU* 3.6 32.8 - - + +
28A GLU* 5.9 0.2 - - - +
104A HIS* 3.0 16.9 + - + +
105A VAL* 3.2 12.1 + - - +
107A ALA* 1.3 74.3 - - - +
109A PHE* 1.3 58.5 + - - +
111A VAL* 3.3 5.4 + - - +
112A ARG* 3.0 32.3 + - - +
111C VAL* 3.9 21.9 - - + +
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Residues in contact with PHE 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LEU* 4.1 5.4 - - + -
27A LEU* 3.7 31.0 - - + -
57A PHE* 3.6 39.0 - - + -
60A ALA* 4.1 12.3 - - + -
61A LEU* 3.7 46.0 - - + -
64A LEU* 4.6 5.2 - - + -
105A VAL* 3.0 45.5 + - + -
106A MSE 3.2 6.9 + - + +
108A ALA* 1.3 73.7 - - - +
110A ALA* 1.3 59.4 + - - +
112A ARG* 3.2 3.1 + - - +
113A ALA* 2.8 30.1 + - - +
119A LEU* 4.0 22.8 - - + +
123A ARG* 5.4 1.1 - - - -
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Residues in contact with ALA 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A MSE 2.9 13.5 + - - +
107A ALA* 3.2 11.0 + - - +
109A PHE* 1.3 75.6 - - - +
111A VAL* 1.3 63.7 + - - +
113A ALA* 3.3 15.2 - - - +
114A ALA 3.8 2.8 + - - -
123A ARG* 3.4 41.2 - - - +
162C LEU* 3.9 21.5 - - + +
165C ILE* 4.6 3.6 - - - +
166C GLY* 4.0 9.2 + - - -
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Residues in contact with VAL 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A ALA 3.0 16.3 + - - +
108A ALA* 3.6 7.9 - - - +
110A ALA* 1.3 76.4 - - - +
112A ARG* 1.3 67.9 + - + +
114A ALA* 3.1 22.3 + - - +
115A THR* 4.4 0.7 + - - -
26C GLY* 6.2 1.6 - - - -
104C HIS* 4.0 15.8 + - + +
107C ALA* 3.8 27.1 - - + +
108C ALA* 3.9 25.8 - - + +
111C VAL* 3.6 22.4 - - + -
162C LEU* 3.9 7.4 - - + -
165C ILE* 4.6 5.4 - - + -
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Residues in contact with ARG 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LEU* 3.4 39.4 + - + +
28A GLU* 3.2 43.4 + - - +
53A LYS* 5.2 6.5 - - - +
57A PHE* 4.6 11.9 - - + -
108A ALA* 3.0 20.6 + - - +
109A PHE 3.2 2.9 + - - +
111A VAL* 1.3 81.0 - - - +
113A ALA* 1.3 56.4 + - - +
115A THR* 3.0 27.0 + - - +
116A SER* 3.1 14.0 + - - -
119A LEU* 3.7 22.0 - - + -
28C GLU* 3.4 48.6 + - - +
112C ARG* 4.9 0.6 - - - +
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Residues in contact with ALA 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A LEU* 6.3 0.2 - - + -
109A PHE 2.8 13.8 + - - +
110A ALA* 3.3 17.9 - - - +
111A VAL 3.1 0.2 - - - -
112A ARG* 1.3 77.7 - - - +
114A ALA* 1.3 60.5 + - - +
115A THR 3.1 1.2 + - - -
116A SER 3.4 14.0 + - - +
119A LEU* 4.0 15.5 - - - +
120A ALA* 3.6 30.0 - - - +
123A ARG* 4.6 4.5 - - + -
165C ILE 4.6 0.3 - - - +
166C GLY* 3.7 18.4 - - - -
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Residues in contact with ALA 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ALA 3.8 2.4 + - - -
111A VAL 3.1 16.7 + - - +
113A ALA* 1.3 77.4 - - - +
115A THR* 1.3 60.4 + - - +
104C HIS* 3.7 30.7 - - + +
165C ILE* 3.7 31.7 + - + +
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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