Contacts of the helix formed by residues 95 - 115 (chain A) in PDB entry 3NC0
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 PRO 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A ILE 3.9 2.7 - - - +
94A LEU* 1.3 84.4 - - + +
96A ARG* 1.3 57.7 + - - +
97A ASN* 3.8 20.2 - - - +
98A GLN* 2.7 61.2 + - + +
99A CYS* 3.2 8.9 + - - -
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Residues in contact with ARG 96 (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 LEU 3.3 4.9 + - - -
95A PRO* 1.3 68.6 - - - +
97A ASN* 1.3 65.0 + - - +
99A CYS* 3.0 24.6 + - - +
100A GLU* 3.1 48.3 + - - +
103A LYS* 5.1 2.2 - - - +
141A GLU* 4.2 10.1 + - - -
145A HIS* 3.0 58.3 + - - +
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Residues in contact with ASN 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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95A PRO* 3.8 17.9 - - - +
96A ARG* 1.3 79.1 - - - +
98A GLN* 1.3 73.5 + - - +
100A GLU* 3.6 14.8 + - - +
101A GLY* 3.0 22.9 + - - -
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Residues in contact with GLN 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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55A GLU* 5.2 3.1 - - - +
56A HIS* 5.2 9.7 + - - -
94A LEU* 3.5 20.4 - - + +
95A PRO* 2.7 49.3 + - + +
97A ASN* 1.3 77.9 + - - +
99A CYS* 1.3 65.2 + - - +
101A GLY* 2.9 11.0 + - - +
102A ILE* 3.0 33.3 - - + +
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Residues in contact with CYS 99 (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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91A TRP* 3.4 66.6 - - + +
94A LEU* 3.5 21.9 - - - +
95A PRO 3.2 9.7 + - - -
96A ARG* 3.0 17.2 + - - +
98A GLN* 1.3 75.3 - - - +
100A GLU* 1.3 59.6 + - + +
102A ILE* 2.8 22.5 + - - +
103A LYS* 3.0 11.2 + - - +
141A GLU* 4.8 4.7 - - - +
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Residues in contact with GLU 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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96A ARG* 3.1 57.2 + - - +
97A ASN* 3.7 14.5 - - - +
99A CYS* 1.3 74.9 - - + +
101A GLY* 1.3 62.8 + - - +
103A LYS* 3.2 31.0 + - + +
104A LYS* 3.2 35.7 + - - +
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Residues in contact with GLY 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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97A ASN 3.0 13.1 + - - -
98A GLN* 2.9 9.9 + - - -
100A GLU* 1.3 77.6 - - - +
102A ILE* 1.3 59.4 + - - +
104A LYS* 3.9 6.4 + - - +
105A TYR* 3.1 26.0 + - - +
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Residues in contact with ILE 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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56A HIS* 5.6 6.7 - - - +
83A LEU* 4.4 17.9 - - + -
87A ILE* 4.3 7.6 - - + -
91A TRP* 3.7 13.9 - - + -
94A LEU* 5.4 4.9 - - + -
98A GLN* 3.0 43.0 + - + +
99A CYS* 2.8 9.0 + - - +
101A GLY* 1.3 78.4 - - - +
103A LYS* 1.3 56.9 + - - +
105A TYR* 2.9 11.8 + - + +
106A VAL* 2.7 44.5 + - + +
137A ILE* 3.5 24.7 - - + -
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Residues in contact with LYS 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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91A TRP* 4.4 7.6 - - + -
96A ARG* 5.1 2.7 - - - +
99A CYS 3.0 18.1 + - - +
100A GLU* 3.3 29.1 + - + +
102A ILE* 1.3 78.5 - - - +
104A LYS* 1.3 61.2 + - + +
106A VAL* 3.7 1.2 - - - +
107A VAL* 2.8 37.4 + - + +
134A LEU* 5.8 0.6 - - - +
137A ILE* 4.5 12.1 - - + -
141A GLU* 3.0 26.6 + - - +
145A HIS 3.3 24.9 + - - -
146A TRP* 3.3 37.1 - - + +
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Residues in contact with LYS 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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100A GLU* 3.2 29.4 + - - +
101A GLY* 4.3 5.3 - - - +
103A LYS* 1.3 76.6 - - + +
105A TYR* 1.3 60.9 + - - +
107A VAL* 4.4 6.1 - - - -
108A GLY* 2.9 28.4 + - - -
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Residues in contact with TYR 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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59A ALA* 5.5 3.6 - - + -
60A TRP* 3.7 25.8 + + + -
63A VAL* 4.1 13.1 - - + +
64A ASP* 2.7 35.2 + - - -
83A LEU* 4.8 19.3 - - + -
101A GLY 3.1 22.2 + - - +
102A ILE* 2.9 14.8 + - + +
104A LYS* 1.3 78.6 - - - +
106A VAL* 1.3 58.3 + - + +
109A LEU* 2.9 51.4 + - + +
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Residues in contact with VAL 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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83A LEU* 4.4 13.7 - - + -
102A ILE* 2.7 37.6 + - + +
103A LYS 3.8 2.0 - - - +
105A TYR* 1.3 74.3 - - + +
107A VAL* 1.3 57.4 + - - +
108A GLY 3.2 1.8 - - - -
109A LEU* 3.0 7.2 + - + +
110A ILE* 2.7 58.4 + - + +
130A LEU* 4.5 9.6 - - + +
133A ILE* 4.2 18.6 - - + -
134A LEU* 4.1 26.0 - - + +
137A ILE* 4.2 5.6 - - + -
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Residues in contact with VAL 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 LYS* 2.8 27.9 + - + +
104A LYS* 4.3 5.2 - - - +
106A VAL* 1.3 74.3 - - - +
108A GLY* 1.3 57.9 + - - +
110A ILE* 3.3 9.1 - - - +
111A ILE* 2.8 48.1 + - + +
134A LEU* 4.5 22.9 - - + -
146A TRP* 4.6 22.7 - - + +
149A PHE* 6.5 0.2 - - + -
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Residues in contact with GLY 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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104A LYS 2.9 16.3 + - - -
107A VAL* 1.3 74.3 - - - +
109A LEU* 1.3 55.3 + - - +
110A ILE 3.0 1.3 - - - -
111A ILE* 3.1 9.2 + - - +
112A LYS* 2.7 37.3 + - - +
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Residues in contact with LEU 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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63A VAL* 4.1 14.6 - - + -
64A ASP* 5.7 0.4 - - - +
80A LEU* 5.6 3.1 - - + -
83A LEU* 5.8 1.6 - - + -
105A TYR* 2.9 60.1 + - + +
106A VAL* 3.0 8.5 + - + +
108A GLY* 1.3 74.1 - - - +
110A ILE* 1.3 53.1 + - - +
112A LYS* 3.6 23.5 - - + +
113A THR* 2.6 38.7 + - + +
126A TYR* 3.3 26.7 - - + +
130A LEU* 4.4 16.4 - - + -
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Residues in contact with ILE 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 VAL* 2.7 32.7 + - + +
107A VAL* 3.3 8.5 - - - +
109A LEU* 1.3 70.0 - - - +
111A ILE* 1.3 62.7 + - + +
113A THR* 2.9 6.1 + - - -
114A SER* 2.3 65.5 + - - +
130A LEU* 4.2 22.0 - - + +
131A ASN* 3.9 11.0 - - - +
134A LEU* 3.5 43.1 - - + -
166A ASN* 3.8 10.5 - - - +
167A ASN* 5.9 0.9 - - - +
170A ILE* 4.9 4.7 - - + -
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Residues in contact with ILE 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 VAL* 2.8 44.8 + - + +
108A GLY* 3.4 8.5 - - - +
110A ILE* 1.3 74.9 - - + +
112A LYS* 1.3 55.7 + - - +
114A SER* 4.4 2.9 - - - -
115A SER* 2.6 54.1 + - - +
163A LEU* 3.7 37.0 - - + -
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Residues in contact with LYS 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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63A VAL 5.5 5.5 + - - -
66A ILE 5.9 0.6 + - - -
108A GLY 2.7 21.0 + - - +
109A LEU* 3.6 21.0 - - + +
111A ILE* 1.3 73.6 - - - +
113A THR* 1.3 74.8 + - + +
115A SER* 3.6 2.4 - - - -
116A ASP* 2.9 24.8 + - - +
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Residues in contact with THR 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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109A LEU* 2.6 21.9 + - + +
110A ILE* 2.9 3.6 + - - -
112A LYS* 1.3 95.2 - - + +
114A SER* 1.3 62.5 + - - +
116A ASP* 2.8 31.7 + - + +
119A CYS* 4.8 4.9 - - - +
122A LYS* 6.1 4.3 - - + -
126A TYR* 3.8 23.8 - - + +
127A ILE* 3.8 26.4 - - - +
130A LEU* 3.3 17.0 - - - +
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Residues in contact with SER 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 ILE* 2.3 59.0 + - - +
111A ILE* 4.2 2.5 - - - -
113A THR* 1.3 67.2 + - - +
115A SER* 1.3 56.9 + - - +
116A ASP 3.1 8.0 + - - +
119A CYS* 5.8 2.9 - - - +
127A ILE* 4.1 11.5 - - - +
130A LEU* 5.9 1.2 - - - +
131A ASN* 4.2 0.5 + - - -
162A SER* 4.5 17.9 - - - +
163A LEU* 5.8 6.7 - - - -
166A ASN* 3.0 30.4 + - - +
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Residues in contact with SER 115 (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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111A ILE* 2.6 31.5 + - - +
112A LYS* 3.6 2.5 - - - -
114A SER* 1.3 70.4 - - - +
116A ASP* 1.3 66.6 + - - +
117A PRO* 3.3 5.2 - - - +
160A SER* 5.5 1.8 + - - -
162A SER* 4.9 13.1 - - - -
163A LEU* 3.5 28.8 - - - +
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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