Contacts of the helix formed by residues 117 - 137 (chain A) in PDB entry 1N8T
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 VAL 117 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A LEU* 4.7 2.2 - - + -
101A ALA* 3.9 27.4 - - + -
110A ILE* 2.8 29.4 + - + +
112A VAL* 3.8 25.1 - - + -
115A LYS* 4.0 10.5 - - + +
116A ASP* 1.3 70.8 - - - +
118A MET* 1.3 72.2 + - - +
119A PRO* 3.3 3.8 - - - -
120A GLU* 2.9 21.9 + - + +
121A VAL* 3.0 11.1 + - + +
268A TRP* 3.7 34.3 - - + +
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Residues in contact with MET 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ALA* 3.3 29.4 - - - +
102A LEU 5.4 0.2 - - - +
104A ASN* 3.5 26.0 - - - +
107A ASN* 3.5 35.4 - - + +
108A THR 3.4 23.3 - - - +
110A ILE* 4.4 2.9 - - - +
116A ASP* 3.1 16.0 + - - +
117A VAL* 1.3 90.0 - - - +
119A PRO* 1.3 63.0 - - + +
121A VAL* 2.9 23.4 + - + +
122A ASN* 2.8 34.4 + - - +
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Residues in contact with PRO 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ASP* 3.5 27.4 - - + +
117A VAL 3.3 5.2 - - - -
118A MET* 1.3 95.7 - - + +
120A GLU* 1.3 65.7 + - + +
122A ASN* 3.9 5.8 - - + +
123A LYS* 2.9 28.6 + - - +
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Residues in contact with GLU 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A LYS* 6.4 2.9 - - + -
116A ASP 5.0 3.8 - - - +
117A VAL* 2.9 17.3 + - + +
119A PRO* 1.3 84.4 - - + +
121A VAL* 1.3 63.9 + - - +
123A LYS* 3.2 30.1 + - - +
124A VAL* 3.2 28.6 + - - +
266A TRP* 3.8 24.7 + - + +
268A TRP* 6.1 0.2 - - + -
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Residues in contact with VAL 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ALA 4.0 20.0 - - - +
102A LEU* 3.7 30.1 - - + +
117A VAL* 3.0 18.2 + - + +
118A MET* 2.9 21.8 + - + +
120A GLU* 1.3 77.1 - - - +
122A ASN* 1.3 60.1 + - - +
124A VAL* 3.4 2.8 + - - +
125A LEU* 2.9 39.4 + - + +
266A TRP* 3.8 13.4 - - + -
268A TRP* 4.0 25.1 - - + -
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Residues in contact with ASN 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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104A ASN 5.4 0.4 + - - -
105A ARG* 4.9 5.5 - - - +
107A ASN* 2.7 37.0 + - - +
118A MET* 2.8 20.3 + - - +
119A PRO* 4.1 5.6 - - + +
121A VAL* 1.3 81.0 - - - +
123A LYS* 1.3 58.5 + - - +
125A LEU* 3.5 24.1 - - - +
126A ASP* 2.7 42.0 + - - +
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Residues in contact with LYS 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A PRO 2.9 17.2 + - - +
120A GLU* 3.2 34.6 + - - +
121A VAL 3.3 0.2 - - - -
122A ASN* 1.3 75.9 - - - +
124A VAL* 1.3 67.8 + - - +
126A ASP* 3.2 8.5 + - - +
127A LYS* 2.8 32.1 + - + +
264A GLU* 3.9 20.2 + - - -
266A TRP* 6.1 0.8 - - - -
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Residues in contact with VAL 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A GLU 3.2 13.9 + - - +
121A VAL 3.7 6.3 - - - +
123A LYS* 1.3 86.8 - - - +
125A LEU* 1.3 59.4 + - - +
127A LYS* 3.1 10.0 + - + +
128A MET* 2.7 52.1 + - + +
263A PHE* 4.6 5.2 - - + -
264A GLU* 3.5 43.1 - - + +
266A TRP* 3.8 13.5 - - + -
278A ALA* 4.0 11.7 - - + +
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Residues in contact with LEU 125 (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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102A LEU 4.2 4.3 - - - +
105A ARG* 4.0 20.2 - - - +
121A VAL* 2.9 27.1 + - + +
122A ASN* 3.2 32.3 + - + +
124A VAL* 1.3 76.1 - - + +
126A ASP* 1.3 59.9 + - - +
128A MET* 2.9 23.6 + - - +
129A LYS 2.8 25.8 + - - -
276A TRP 4.8 5.8 - - - +
277A SER* 5.8 1.3 - - - -
289A PHE* 3.3 21.2 - - + -
292A PHE* 4.0 23.3 - - + -
296A LEU* 4.2 11.2 - - + -
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Residues in contact with ASP 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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122A ASN* 2.7 30.0 + - - +
123A LYS* 3.5 7.3 - - - +
125A LEU* 1.3 73.6 - - - +
127A LYS* 1.3 63.8 + - - +
129A LYS* 3.2 11.4 + - - +
130A ALA* 3.0 23.2 + - - +
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Residues in contact with LYS 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A LYS* 2.8 19.3 + - + +
124A VAL* 3.5 11.7 - - + +
125A LEU 3.1 0.2 - - - -
126A ASP* 1.3 77.6 - - - +
128A MET* 1.3 62.0 + - - +
130A ALA* 3.3 7.1 + - + +
131A PHE* 3.2 19.1 + - - +
259A PRO 5.0 0.6 + - - -
260A GLN* 2.8 44.3 + - - +
262A MET 3.8 20.3 + - - +
263A PHE* 3.6 32.2 - - + -
264A GLU 5.8 0.7 - - - +
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Residues in contact with MET 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A VAL* 2.7 35.4 + - + +
125A LEU* 3.3 25.1 - - - +
127A LYS* 1.3 73.6 - - - +
129A LYS* 1.3 62.4 + - - +
131A PHE* 3.6 1.6 + - - +
132A CYS* 3.1 25.1 + - - +
263A PHE* 3.8 22.9 - - + -
277A SER 3.6 18.2 - - - +
278A ALA* 3.6 26.0 - - - +
280A GLY 4.1 0.9 - - - +
281A LEU* 3.9 33.9 - - + +
284A ALA* 4.8 1.1 - - + -
289A PHE* 3.7 10.5 - - + -
292A PHE* 4.1 20.6 - - + -
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Residues in contact with LYS 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A LEU 2.8 9.6 + - - +
126A ASP* 3.2 13.0 + - - +
128A MET* 1.3 78.3 - - - +
130A ALA* 1.3 56.9 + - - +
132A CYS* 3.2 3.6 + - - +
133A GLN* 2.9 52.6 + - + +
289A PHE* 3.6 48.0 - - + -
290A ASP* 5.7 6.1 + - - -
293A GLU* 5.0 10.1 + - - +
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Residues in contact with ALA 130 (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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126A ASP 3.0 15.2 + - - +
127A LYS* 3.8 7.2 - - + +
129A LYS* 1.3 76.6 - - - +
131A PHE* 1.3 56.9 + - - +
133A GLN* 3.3 21.1 + - - +
134A ARG* 2.9 35.0 + - + +
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Residues in contact with PHE 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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127A LYS 3.2 7.7 + - - +
128A MET 4.1 0.9 - - - +
130A ALA* 1.3 75.3 - - - +
132A CYS* 1.3 64.7 + - - +
134A ARG* 3.1 9.1 + - - +
135A VAL* 2.9 50.1 + - + +
140A TRP* 3.6 41.1 - + - -
204A LEU* 3.5 28.7 - - + -
243A VAL* 3.7 17.5 - - + -
261A ASN* 5.1 3.6 - - - -
263A PHE* 3.5 33.2 - + + -
281A LEU* 3.7 31.2 - - + -
285A LEU* 4.3 6.5 - - + -
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Residues in contact with CYS 132 (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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128A MET 3.1 20.0 + - - +
129A LYS* 3.5 5.6 - - - +
131A PHE* 1.3 74.0 - - - +
133A GLN* 1.3 66.5 + - - +
135A VAL* 3.1 1.2 + - - +
136A ARG* 2.9 44.7 + - - +
281A LEU* 5.2 2.2 - - + -
284A ALA* 3.4 33.2 - - + -
285A LEU* 3.9 19.3 - - + -
289A PHE* 4.1 21.5 - - + -
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Residues in contact with GLN 133 (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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129A LYS* 2.9 47.9 + - + +
130A ALA* 3.4 18.4 + - - +
132A CYS* 1.3 76.7 - - - +
134A ARG* 1.3 59.2 + - + +
135A VAL 3.1 0.9 + - - -
136A ARG* 5.1 2.9 - - - +
137A SER* 2.7 37.2 + - - -
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Residues in contact with ARG 134 (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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130A ALA* 2.9 20.8 + - + +
131A PHE* 3.1 13.4 + - - +
133A GLN* 1.3 80.2 - - + +
135A VAL* 1.3 58.6 + - - +
137A SER* 4.1 3.1 - - - -
139A ASP* 2.8 44.9 + - - +
140A TRP* 2.7 69.9 + - + +
141A LYS 5.4 0.2 - - - +
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Residues in contact with VAL 135 (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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131A PHE* 2.9 54.5 + - + +
132A CYS 3.1 0.4 + - - +
134A ARG* 1.3 79.7 - - - +
136A ARG* 1.3 65.2 + - - +
137A SER 3.3 1.1 + - - -
138A GLY* 3.5 10.9 + - - -
140A TRP* 4.1 16.2 - - + +
147A THR* 5.6 0.2 - - - -
148A ILE* 4.0 39.5 + - + +
151A VAL* 5.0 0.7 - - + -
178A PRO* 4.9 8.3 - - + -
204A LEU* 4.0 8.3 - - + -
285A LEU* 3.8 20.9 - - + -
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Residues in contact with ARG 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A CYS* 2.9 32.4 + - - +
133A GLN* 4.4 2.7 - - - +
135A VAL* 1.3 78.0 - - - +
137A SER* 1.3 61.8 + - - +
138A GLY 3.3 0.4 + - - -
173A TYR 4.7 0.2 + - - -
174A SER* 4.6 0.4 - - - +
175A SER 4.1 16.0 + - - -
176A GLY* 4.2 18.9 + - - +
177A GLY* 3.5 15.6 - - - +
178A PRO* 4.5 12.6 - - + -
285A LEU* 2.8 23.0 + - + +
286A HIS 2.7 29.3 + - - -
287A VAL* 3.3 4.2 + - - +
288A GLY* 3.0 28.2 - - - +
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Residues in contact with SER 137 (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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133A GLN* 2.7 22.4 + - - -
134A ARG* 4.1 0.2 - - - -
136A ARG* 1.3 79.9 - - - +
138A GLY* 1.3 57.6 + - - +
139A ASP* 3.4 19.9 + - - +
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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
------------------------------------------------------------
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