Contacts of the helix formed by residues 122 - 143 (chain A) in PDB entry 2HKU
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 ARG 122 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A GLU* 5.6 7.2 - - - +
118A MSE 3.2 19.2 + - - -
119A THR* 3.1 16.2 - - - +
120A GLY* 3.0 31.9 - - - +
121A ARG* 1.3 72.9 - - - +
123A SER* 1.3 61.9 + - - +
124A GLU* 3.2 22.4 - - - +
125A LEU* 3.0 22.9 + - + +
126A ARG* 2.9 26.0 + - - +
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Residues in contact with SER 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ARG 2.9 11.0 + - - -
122A ARG* 1.3 65.9 - - - +
124A GLU* 1.3 73.0 + - - +
125A LEU 2.5 4.4 + - - -
126A ARG* 4.1 11.7 - - - +
127A ASP* 3.0 33.5 + - - -
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Residues in contact with GLU 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A SER* 5.0 3.5 + - - -
63A ARG* 3.8 33.5 + - - +
122A ARG* 3.6 27.9 - - + +
123A SER* 1.3 82.6 + - - +
125A LEU* 1.3 82.6 + - + +
127A ASP* 3.3 19.9 + - - +
128A LEU* 3.6 6.1 + - - +
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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
----------------------------------------------------------
62A GLU* 4.2 19.7 - - + -
63A ARG* 3.8 32.5 - - + +
66A VAL* 4.0 25.9 - - + +
118A MSE 5.4 1.8 - - + -
119A THR* 4.6 12.6 - - + -
122A ARG* 3.3 37.0 - - + +
123A SER 2.5 2.0 + - - -
124A GLU* 1.3 101.1 - - + +
126A ARG* 1.3 67.1 + - - +
127A ASP 3.2 0.2 - - - -
128A LEU* 3.3 25.2 + - + +
129A ILE* 3.3 16.7 + - - +
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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
----------------------------------------------------------
119A THR* 4.5 7.1 - - - +
120A GLY 4.8 10.5 - - - +
121A ARG* 5.2 3.1 - - - +
122A ARG 2.9 16.6 + - - +
123A SER* 4.0 10.5 - - - +
125A LEU* 1.3 77.1 - - - +
127A ASP* 1.3 64.2 + - - +
129A ILE* 3.3 8.4 + - - +
130A THR* 2.8 50.7 + - - +
177B LYS 5.3 1.6 + - - -
179B ALA* 2.9 45.6 + - + +
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Residues in contact with ASP 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A SER* 3.0 28.5 + - - +
124A GLU* 3.3 12.1 - - - +
125A LEU 3.2 0.2 - - - -
126A ARG* 1.3 82.3 + - - +
128A LEU* 1.3 60.4 + - + +
130A THR* 3.6 9.3 + - - -
131A ASP* 2.9 38.9 + - - +
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Residues in contact with LEU 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ARG* 4.1 30.1 - - - +
66A VAL* 3.7 26.0 - - + -
67A GLU* 3.8 29.6 - - + +
70A CYS* 4.0 8.3 - - + -
124A GLU 3.6 5.0 + - - +
125A LEU* 3.3 24.5 + - + +
127A ASP* 1.3 75.5 - - + +
129A ILE* 1.3 57.8 + - - +
131A ASP* 3.9 4.1 - - - +
132A THR* 2.6 38.7 + - - -
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Residues in contact with ILE 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A VAL* 4.0 17.9 - - + -
70A CYS* 4.1 3.8 - - - -
112A PHE* 3.7 22.0 - - + -
115A ALA* 4.0 7.2 - - + -
116A MSE 3.7 39.0 - - + +
119A THR* 3.6 22.9 - - + +
125A LEU 3.3 10.3 + - - +
126A ARG 3.3 8.6 + - - +
128A LEU* 1.3 80.6 - - - +
130A THR* 1.4 60.4 + - + +
132A THR* 3.2 3.6 + - - -
133A LEU* 2.9 36.0 + - + +
176B GLN 5.8 0.2 - - - +
179B ALA* 3.9 19.1 - - + -
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Residues in contact with THR 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ARG* 2.8 45.4 + - - +
127A ASP* 3.6 12.5 + - - -
129A ILE* 1.4 69.4 - - + +
131A ASP* 1.3 70.9 + - - +
133A LEU* 3.8 9.6 - - + +
134A ARG* 3.0 35.2 + - - +
179B ALA* 3.8 28.9 - - + +
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Residues in contact with ASP 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ASP* 2.9 25.4 + - - +
128A LEU* 3.9 4.6 - - - +
130A THR* 1.3 81.9 + - - +
132A THR* 1.3 56.5 + - - +
134A ARG* 3.4 13.7 + - - +
135A THR* 3.0 33.2 + - - +
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Residues in contact with THR 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A CYS* 3.1 32.3 - - - +
73A VAL* 3.4 32.3 - - + -
74A LEU* 3.9 17.2 - - + +
112A PHE* 3.6 12.3 - - + -
128A LEU 2.6 21.8 + - - -
129A ILE 3.6 4.3 - - - -
130A THR 3.2 0.2 - - - -
131A ASP* 1.3 73.1 - - - +
133A LEU* 1.3 59.5 + - - +
135A THR* 3.3 7.7 + - - -
136A LEU* 2.9 32.1 + - + +
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Residues in contact with LEU 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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112A PHE* 3.7 26.9 - - + -
116A MSE 4.0 9.9 - - - -
129A ILE* 2.9 25.7 + - + +
130A THR* 3.8 9.6 - - + +
131A ASP 3.3 0.2 - - - -
132A THR* 1.3 73.4 - - - +
134A ARG* 1.3 66.9 + - + +
136A LEU* 3.4 5.7 + - + +
137A HIS* 3.0 36.2 + - + +
171A PHE* 3.8 25.4 - - + -
176B GLN* 3.8 41.3 - - + +
179B ALA 5.3 3.6 - - - -
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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
----------------------------------------------------------
130A THR* 3.0 28.5 + - - +
131A ASP* 3.6 14.4 - - - +
133A LEU* 1.3 77.0 - - + +
135A THR* 1.3 54.3 + - - +
137A HIS* 3.4 8.4 + - - +
138A SER* 2.8 39.2 + - - +
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Residues in contact with THR 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LEU* 3.9 24.5 - - + +
131A ASP* 3.0 14.0 + - - +
132A THR* 3.6 9.1 - - - -
133A LEU 3.2 0.2 - - - -
134A ARG* 1.3 78.0 - - - +
136A LEU* 1.4 56.9 + - - +
138A SER* 3.8 6.0 - - - -
139A SER* 2.8 39.8 + - - -
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Residues in contact with LEU 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A VAL* 3.9 35.7 - - + +
74A LEU* 4.0 16.4 - - + -
77A GLY* 5.0 3.8 - - - -
112A PHE* 3.8 28.7 - - + -
132A THR 2.9 19.5 + - - +
133A LEU* 3.4 6.5 + - + +
135A THR* 1.4 74.8 - - - +
137A HIS* 1.3 59.7 + - + +
139A SER* 2.6 24.1 + - - +
140A GLY 3.0 10.0 + - - -
167A TRP* 3.1 44.4 + - + +
171A PHE* 4.0 15.5 - - + -
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Residues in contact with HIS 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 LEU* 3.0 34.9 + - + +
134A ARG* 3.7 7.6 - - - +
136A LEU* 1.3 76.0 - - + +
138A SER* 1.3 64.7 + - - +
140A GLY 3.1 2.1 + - - -
141A GLU* 3.2 10.5 + - - +
160A ASP 5.6 0.2 - - - +
163A SER* 2.6 31.0 + - - +
164A LYS* 3.7 50.1 - - + +
167A TRP* 3.6 32.8 - + + +
176B GLN* 3.4 30.4 + - - -
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Residues in contact with SER 138 (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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134A ARG* 2.8 24.7 + - - +
135A THR* 3.8 7.2 - - - -
137A HIS* 1.3 68.7 - - - +
139A SER* 1.3 67.8 + - - +
140A GLY 3.1 0.7 + - - -
141A GLU* 3.2 19.3 + - - +
142A VAL* 3.2 27.3 + - - +
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Residues in contact with SER 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A GLY* 6.0 0.9 - - - -
81A GLU* 3.5 17.0 + - - -
135A THR* 2.8 20.0 + - - -
136A LEU* 2.6 27.0 + - - +
138A SER* 1.3 77.8 - - - +
140A GLY* 1.3 55.2 + - - +
142A VAL* 3.4 10.2 + - - +
143A ALA* 3.0 33.8 + - - +
167A TRP* 4.9 0.2 - - - -
302A EDO 3.0 12.0 + - - -
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Residues in contact with GLY 140 (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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136A LEU 3.0 10.2 + - - -
137A HIS 3.1 0.8 + - - -
138A SER 3.0 0.6 - - - -
139A SER* 1.3 75.6 - - - +
141A GLU* 1.4 64.1 + - - +
142A VAL 3.4 0.3 + - - -
144A LEU* 3.5 5.9 + - - +
145A ILE* 3.0 27.3 + - - +
163A SER* 3.2 17.0 - - - -
166A PHE* 5.8 0.7 - - - -
167A TRP* 4.5 1.3 - - - -
302A EDO 3.4 24.2 - - - -
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Residues in contact with GLU 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A HIS* 3.2 18.3 + - - +
138A SER* 3.5 17.0 + - - +
140A GLY* 1.4 75.8 - - - +
142A VAL* 1.3 63.9 + - + +
145A ILE* 4.1 5.4 - - - -
146A ARG* 3.0 28.6 + - - +
159A ILE* 3.5 46.5 - - + +
160A ASP* 3.3 28.3 - - - +
163A SER* 3.4 4.1 + - - -
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Residues in contact with VAL 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A SER* 3.2 16.4 + - - +
139A SER* 3.7 14.6 - - - +
141A GLU* 1.3 86.4 - - + +
143A ALA* 1.3 65.4 + - + +
146A ARG* 3.5 39.6 + - - +
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Residues in contact with ALA 143 (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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81A GLU* 3.4 21.8 - - + +
93A TYR* 3.2 15.5 - - - +
139A SER 3.0 16.1 + - - +
142A VAL* 1.3 82.1 - - + +
144A LEU* 1.4 66.1 + - - +
145A ILE 3.5 0.3 + - - -
146A ARG 3.6 1.2 + - - -
147A THR* 2.9 26.8 + - - -
302A EDO 3.4 9.6 - - - +
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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