Contacts of the helix formed by residues 115 - 131 (chain A) in PDB entry 5NKS
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 SER 115 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A PRO* 4.5 0.7 - - - -
113A GLY 4.0 2.0 + - - -
114A VAL* 1.3 78.2 - - - +
116A LEU* 1.3 66.7 + - - +
117A LEU* 3.5 4.3 + - - +
118A ALA* 3.0 26.2 + - - +
119A ALA* 3.0 22.0 + - - +
151A GLU* 3.5 19.1 + - - -
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Residues in contact with LEU 116 (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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108A VAL* 4.7 2.3 - - - +
110A PRO* 3.8 15.3 - - + -
114A VAL 5.6 0.2 - - - +
115A SER* 1.3 75.0 - - - +
117A LEU* 1.3 59.2 + - - +
119A ALA* 3.4 5.3 + - - +
120A TYR* 2.9 29.2 + - - +
139A VAL* 4.0 16.8 - - + +
140A ASP 3.5 24.0 - - - +
141A ILE* 4.4 13.5 - - + -
142A THR 5.0 1.3 - - - +
148A ILE* 3.7 25.8 - - + -
151A GLU* 3.3 17.6 + - + +
152A LEU* 3.8 27.1 - - + -
155A LEU* 4.0 14.0 - - + +
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Residues in contact with LEU 117 (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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115A SER* 3.3 3.1 - - - +
116A LEU* 1.3 76.7 - - - +
118A ALA* 1.3 62.9 + - - +
120A TYR* 3.3 6.6 + - + +
121A GLU* 3.0 30.5 + - + +
151A GLU* 3.0 27.7 + - + +
154A ALA* 4.1 23.1 - - + -
155A LEU* 3.7 29.8 - - + -
159A LYS* 4.1 25.1 - - + -
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Residues in contact with ALA 118 (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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114A VAL* 3.8 16.8 - - + -
115A SER* 3.0 20.2 + - - +
117A LEU* 1.3 78.1 - - - +
119A ALA* 1.3 63.3 + - - +
121A GLU* 3.3 7.8 + - - +
122A GLN* 3.0 28.2 + - - +
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Residues in contact with ALA 119 (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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108A VAL* 3.6 19.3 - - + -
110A PRO* 3.7 27.4 - - + -
114A VAL* 3.7 4.8 - - + +
115A SER 3.0 17.9 + - - +
116A LEU* 3.8 3.1 - - - +
118A ALA* 1.3 74.3 - - - +
120A TYR* 1.3 65.2 + - - +
122A GLN* 3.2 15.2 + - - +
123A TRP* 2.9 31.8 + - + -
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Residues in contact with TYR 120 (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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108A VAL* 3.7 12.7 - - + +
116A LEU 2.9 17.6 + - - +
117A LEU* 3.5 5.4 - - + +
119A ALA* 1.3 74.7 - - - +
121A GLU* 1.3 80.7 + - + +
123A TRP* 3.2 3.6 + - - +
124A ARG* 2.9 65.7 + - + +
137A LEU* 3.9 21.8 - - + -
139A VAL* 4.6 7.4 - - + -
155A LEU* 4.1 14.6 - - + -
159A LYS* 2.8 51.7 + - + +
161A VAL* 3.8 22.0 - - + -
468A PHE* 3.5 5.9 - + - -
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Residues in contact with GLU 121 (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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117A LEU* 3.0 23.1 + - + +
118A ALA* 3.3 7.6 + - - +
119A ALA 3.2 0.2 - - - -
120A TYR* 1.3 92.9 - - + +
122A GLN* 1.3 63.0 + - - +
124A ARG* 3.3 8.5 + - - +
125A GLU* 2.9 24.1 + - - +
159A LYS* 3.1 28.8 + - - -
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Residues in contact with GLN 122 (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 ASP* 5.6 3.5 + - - +
114A VAL* 3.8 27.8 - - - +
118A ALA* 3.0 21.5 + - - +
119A ALA* 3.2 14.9 + - - +
121A GLU* 1.3 75.5 - - - +
123A TRP* 1.3 72.6 + - - +
125A GLU* 3.3 12.4 + - - +
126A ARG* 3.1 43.5 + - - +
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Residues in contact with TRP 123 (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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77A GLN* 3.6 41.5 - - + +
78A MET* 4.0 2.7 - - - -
79A PRO* 4.3 4.9 - - + -
89A PHE* 4.6 7.6 - + - -
106A ASP* 2.9 28.3 + - - -
107A HIS 3.3 19.7 + - - -
108A VAL* 3.6 23.6 - - + -
109A PHE* 3.3 36.8 - - + -
119A ALA* 2.9 32.1 + - + +
120A TYR 3.6 6.3 - - - +
122A GLN* 1.3 88.4 - - + +
124A ARG* 1.3 57.1 + - - +
126A ARG* 3.3 27.3 + - - +
127A ALA* 2.8 33.5 + - - +
137A LEU* 3.7 23.3 - - + -
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Residues in contact with ARG 124 (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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120A TYR* 2.9 59.5 + - + +
121A GLU* 3.3 10.5 + - - +
123A TRP* 1.3 76.2 - - - +
125A GLU* 1.3 58.2 + - - +
128A ASP* 2.8 61.7 + - - +
135A TYR* 3.3 21.9 + - - -
137A LEU* 3.8 9.2 - - + -
468A PHE* 3.6 39.7 - - - +
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Residues in contact with GLU 125 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A GLU 2.9 17.1 + - - +
122A GLN* 3.6 10.5 - - - +
123A TRP 3.2 0.4 - - - -
124A ARG* 1.3 77.8 - - - +
126A ARG* 1.3 71.1 + - + +
128A ASP* 4.3 2.5 - - - +
129A SER* 3.3 20.8 + - - -
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Residues in contact with ARG 126 (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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77A GLN* 2.4 61.7 + - + +
84A THR* 5.8 4.4 - - - +
89A PHE* 5.1 1.6 - - - -
122A GLN* 3.1 32.5 + - - +
123A TRP* 3.3 45.0 - - - +
125A GLU* 1.3 85.0 - - + +
127A ALA* 1.3 60.3 + - - +
129A SER* 3.3 10.0 + - - -
130A ALA* 3.3 22.6 - - - +
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Residues in contact with ALA 127 (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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89A PHE* 3.5 33.0 - - + -
123A TRP 2.8 23.4 + - - +
126A ARG* 1.3 71.4 - - - +
128A ASP* 1.3 61.9 + - - +
131A ALA* 2.8 35.1 + - - +
135A TYR* 3.3 32.1 - - + -
137A LEU* 5.4 0.7 - - + -
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Residues in contact with ASP 128 (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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124A ARG* 2.8 58.7 + - - +
125A GLU* 4.3 3.7 - - - +
127A ALA* 1.3 73.6 - - - +
129A SER* 1.3 58.5 + - - +
135A TYR* 2.4 34.0 + - - -
464A GLY* 3.5 21.0 - - - +
466A GLY 4.4 6.0 - - - +
468A PHE* 4.2 4.2 + - - +
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Residues in contact with SER 129 (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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125A GLU 3.3 16.9 + - - -
126A ARG* 3.3 7.8 + - - -
127A ALA 3.1 0.4 - - - -
128A ASP* 1.3 79.8 - - - +
130A ALA* 1.3 58.0 + - - +
463A PRO* 3.7 7.1 - - - +
464A GLY* 3.4 16.2 + - - -
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Residues in contact with ALA 130 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A GLN* 6.0 0.4 - - - +
88A ASP* 6.0 1.1 - - - +
89A PHE* 4.2 6.5 - - + -
90A CYS* 3.4 38.8 - - + +
126A ARG 3.3 16.4 + - - +
127A ALA 3.1 1.0 + - - -
129A SER* 1.3 81.2 - - - +
131A ALA* 1.3 65.7 + - - +
132A CYS 3.3 2.8 + - - -
463A PRO* 3.5 14.1 - - - +
464A GLY 3.4 4.7 - - - +
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Residues in contact with ALA 131 (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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89A PHE* 3.8 20.8 - - + -
93A THR* 3.9 6.7 - - + -
127A ALA 2.8 22.8 + - - +
130A ALA* 1.3 69.7 - - - +
132A CYS* 1.3 59.5 + - - +
133A CYS 3.3 17.9 - - - +
135A TYR* 3.9 14.6 - - + -
464A GLY* 2.9 20.0 + - - +
466A GLY* 2.9 23.0 + - - +
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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