Contacts of the helix formed by residues 114 - 128 (chain B) in PDB entry 1NUA
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 GLY 114 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B ILE* 4.4 5.1 - - - +
113B GLY* 1.3 74.4 - - - +
115B GLY* 1.3 58.2 + - - -
116B VAL* 3.2 3.3 - - - +
117B ILE* 3.1 7.5 + - - +
118B GLY* 2.6 34.8 + - - -
139B THR* 4.4 1.6 - - - -
140B THR* 3.8 27.4 - - - +
143B ALA* 3.9 6.5 - - - -
147B SER* 4.5 0.7 - - - -
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Residues in contact with GLY 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B GLY* 1.3 69.3 - - - -
116B VAL* 1.3 56.9 + - - +
119B ASP* 2.8 43.5 + - - +
140B THR* 4.4 2.2 + - - +
142B LEU* 5.8 7.1 - - - +
143B ALA* 3.9 6.9 - - - +
147B SER* 3.5 22.2 + - - -
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Residues in contact with VAL 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B GLY 3.4 20.9 - - - +
81B GLU* 3.5 34.8 - - + +
83B SER* 3.7 13.7 - - - +
84B LYS* 3.9 24.4 - - + +
114B GLY* 3.2 0.8 - - - -
115B GLY* 1.3 74.5 - - - +
117B ILE* 1.3 68.3 + - + +
119B ASP* 4.2 0.9 - - - +
120B LEU* 3.2 25.2 + - + +
161B LYS* 5.8 1.6 - - - +
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Residues in contact with ILE 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B VAL* 3.8 15.0 - - + +
43B THR* 3.6 26.9 - - - +
44B ASP* 3.6 19.5 - - + +
47B ILE* 4.8 0.4 - - + -
77B ARG* 5.1 4.9 - - + -
83B SER* 5.0 5.8 - - - +
111B ALA 4.1 1.8 - - - -
112B LEU 3.5 28.7 - - - +
113B GLY* 3.7 22.4 - - - +
114B GLY 3.1 5.3 + - - +
116B VAL* 1.3 84.2 - - + +
118B GLY* 1.3 64.0 + - - +
120B LEU* 4.8 6.3 - - + -
121B THR* 2.6 42.8 + - - +
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Residues in contact with GLY 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B ALA* 4.4 5.1 - - - +
113B GLY 4.9 1.3 - - - -
114B GLY 2.6 20.7 + - - -
115B GLY* 3.7 1.1 - - - -
117B ILE* 1.3 74.0 - - - +
119B ASP* 1.3 57.2 + - - +
122B GLY* 2.8 29.1 + - - -
136B GLN* 4.0 30.6 + - - -
147B SER* 5.1 4.9 - - - -
152B LYS 5.7 0.4 - - - -
153B THR* 4.7 1.4 - - - +
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Residues in contact with ASP 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ARG* 5.4 1.7 + - - -
84B LYS* 2.9 30.7 + - - -
115B GLY* 2.8 31.3 + - - +
116B VAL 4.2 0.2 - - - +
118B GLY* 1.3 70.4 - - - +
120B LEU* 1.3 66.8 + - - +
123B PHE* 3.1 16.8 + - - +
147B SER* 4.5 9.8 + - - +
152B LYS 3.6 16.9 - - - +
153B THR* 3.5 4.6 - - - +
154B ALA 3.2 35.1 + - - +
162B ASN* 4.3 4.9 + - - -
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Residues in contact with LEU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B VAL* 5.1 5.4 - - + -
77B ARG* 5.0 4.5 - - + -
83B SER* 3.1 34.5 - - - +
84B LYS* 4.5 6.5 - - - -
85B SER 4.2 0.2 - - - +
88B THR* 3.8 4.9 - - + -
89B LYS* 3.9 31.0 - - + +
92B ILE* 3.7 25.6 - - + -
116B VAL* 3.2 17.6 + - + +
117B ILE* 4.1 6.5 - - + +
119B ASP* 1.3 76.4 - - - +
121B THR* 1.3 67.8 + - - +
123B PHE* 3.1 5.0 + - - +
124B VAL* 2.9 27.5 + - + +
154B ALA 3.7 6.5 + - - -
155B ILE* 3.9 17.3 - - + -
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Residues in contact with THR 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B VAL* 3.5 21.4 - - + +
92B ILE* 5.8 0.2 - - - -
109B VAL* 3.3 33.3 - - + +
110B ILE 3.9 2.9 - - - +
111B ALA* 3.5 28.0 - - + -
117B ILE* 2.6 36.1 + - - +
120B LEU* 1.3 77.1 - - - +
122B GLY* 1.3 64.1 + - - +
124B VAL* 3.1 17.8 + - - +
125B ALA* 3.2 13.5 + - - +
134B TYR* 4.9 2.9 - - + -
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Residues in contact with GLY 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B GLY 2.8 21.6 + - - -
121B THR* 1.3 73.6 - - - +
123B PHE* 1.3 59.5 + - - +
125B ALA* 3.6 3.5 + - - +
126B SER* 3.2 21.5 + - - -
134B TYR* 3.3 29.3 - - - -
153B THR* 3.4 16.3 - - - +
168B TRP* 4.0 5.5 - - - -
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Residues in contact with PHE 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A THR* 3.7 26.7 - - + -
89B LYS* 3.3 36.3 - - + -
119B ASP 3.1 17.9 + - - +
120B LEU 3.1 5.6 + - - +
122B GLY* 1.3 74.5 - - - +
124B VAL* 1.3 64.7 + - - +
126B SER* 2.6 25.8 + - - -
127B THR* 3.6 13.1 + - + -
153B THR* 3.3 10.3 - - - +
154B ALA* 3.7 3.8 - - - +
155B ILE* 3.9 21.1 - - + -
164B ILE* 3.5 31.0 - - + -
165B GLY* 3.5 26.9 - - - -
166B ALA* 3.9 4.5 - - + -
602B CL 3.9 4.5 - - + -
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Residues in contact with VAL 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B VAL* 6.5 0.2 - - + -
89B LYS* 3.8 31.9 - - + +
92B ILE* 3.9 24.9 - - + -
93B GLU* 3.8 21.0 - - + +
96B MET* 4.3 13.0 - - + -
109B VAL* 5.9 3.8 - - + -
120B LEU* 2.9 32.3 + - + +
121B THR* 3.1 10.9 + - + +
123B PHE* 1.3 77.6 - - - +
125B ALA* 1.3 59.4 + - - +
127B THR* 3.3 4.7 + - - -
128B TYR* 2.9 28.4 + - + +
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Residues in contact with ALA 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B MET* 6.3 0.2 - - - -
109B VAL* 3.9 16.6 - - + +
121B THR 3.2 11.2 + - - +
122B GLY 3.9 4.7 - - - +
124B VAL* 1.3 77.6 - - - +
126B SER* 1.3 65.0 + - - +
127B THR 3.2 0.5 + - - -
128B TYR* 3.5 2.8 + - - -
131B GLY* 3.4 1.6 - - - -
132B VAL* 2.9 59.7 + - + +
134B TYR* 3.9 16.4 - - + -
168B TRP* 3.8 2.2 - - + -
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Residues in contact with SER 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A GLY 4.0 1.2 - - - +
166A ALA* 4.8 5.0 - - - +
122B GLY 3.2 7.9 + - - -
123B PHE* 2.6 37.6 + - - -
125B ALA* 1.3 79.8 - - - +
127B THR* 1.3 61.6 + - - +
130B ARG 3.6 3.6 - - - +
131B GLY* 3.3 17.5 + - - -
153B THR* 4.7 0.2 - - - -
166B ALA* 4.0 12.7 - - - +
168B TRP* 3.4 47.0 - - - +
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Residues in contact with THR 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A PHE* 3.9 20.9 - - + -
127A THR* 4.3 3.6 - - + -
164A ILE* 3.3 12.2 - - - +
165A GLY 3.0 26.1 + - - +
166A ALA* 5.0 3.4 - - + -
89B LYS* 2.8 25.9 + - - +
93B GLU* 3.1 6.9 + - - -
123B PHE* 3.7 21.1 - - + -
124B VAL 3.3 2.7 + - - -
125B ALA 3.1 0.2 - - - -
126B SER* 1.3 94.2 + - - +
128B TYR* 1.3 65.6 + - - +
129B MET 2.8 4.5 + - - -
130B ARG 2.9 9.6 + - - -
166B ALA* 5.5 1.1 - - + -
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Residues in contact with TYR 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A LEU 4.2 1.3 - - - -
164A ILE* 4.3 14.4 - - + -
93B GLU* 3.9 12.1 - - + -
96B MET* 3.0 64.4 + - + -
97B LEU* 3.0 35.6 - - + +
102B PRO* 5.1 0.2 - - - +
103B CYS* 2.8 33.1 + - + +
104B GLY 4.0 2.2 - - - -
107B THR* 5.3 0.2 - - - -
124B VAL 2.9 18.0 + - - +
125B ALA* 3.5 2.1 + - - -
127B THR* 1.3 72.7 + - - +
129B MET* 1.3 83.8 + - + +
131B GLY 2.9 10.9 + - - -
132B VAL* 3.4 39.2 - - + +
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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