Contacts of the helix formed by residues 124 - 142 (chain A) in PDB entry 1MHQ
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 THR 124 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A GLU* 2.4 53.9 + - + +
122A TRP 3.8 3.1 + - - +
123A ALA* 1.3 78.4 - - - +
125A GLY* 1.3 64.5 + - - +
126A LYS* 3.9 2.2 - - - -
127A VAL* 3.3 17.2 + - - +
128A LYS* 3.1 21.9 + - - +
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Residues in contact with GLY 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A THR* 1.3 72.5 - - - +
126A LYS* 1.3 60.3 + - - +
128A LYS* 3.7 14.5 - - - +
129A GLY* 2.9 27.2 + - - -
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Residues in contact with LYS 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A GLU* 3.2 28.9 - - - +
80A LEU* 4.4 23.1 - - + -
124A THR* 3.6 0.8 - - - +
125A GLY* 1.3 77.4 - - - +
127A VAL* 1.3 63.3 + - - +
129A GLY* 3.2 1.4 + - - -
130A ARG* 3.0 25.0 + - + +
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Residues in contact with VAL 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ILE 4.3 13.2 - - - +
76A GLU* 3.9 9.6 - - + -
79A ALA* 3.7 22.4 - - + -
80A LEU* 3.7 21.5 - - + -
83A LEU* 4.0 13.2 - - + -
113A VAL* 4.0 19.3 - - + -
123A ALA* 4.0 8.5 - - + -
124A THR* 3.3 27.2 + - - +
125A GLY 3.2 0.2 - - - -
126A LYS* 1.3 80.5 - - - +
128A LYS* 1.3 64.1 + - - +
130A ARG* 3.1 5.2 + - - +
131A VAL* 2.9 22.1 + - + +
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Residues in contact with LYS 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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113A VAL* 3.8 32.8 - - + +
114A LEU* 3.6 21.4 - - + +
115A SER 4.6 10.5 + - - -
121A SER* 4.3 8.9 + - - -
123A ALA 3.4 22.4 + - - +
124A THR 3.1 12.2 + - - +
125A GLY* 3.7 12.7 - - - +
126A LYS 3.3 0.2 - - - -
127A VAL* 1.3 76.1 - - - +
129A GLY* 1.3 63.8 + - - +
131A VAL* 3.1 3.2 + - - +
132A ILE* 2.9 31.9 + - + +
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Residues in contact with GLY 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A GLY 2.9 14.5 + - - -
126A LYS 3.7 3.4 - - - -
128A LYS* 1.3 75.9 - - - +
130A ARG* 1.3 63.8 + - - +
132A ILE* 3.2 10.6 + - - +
133A GLU* 2.8 25.2 + - - +
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Residues in contact with ARG 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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80A LEU* 4.2 16.1 + - + +
83A LEU* 3.7 19.1 - - + +
84A THR* 3.4 36.5 + - - +
87A GLU* 2.4 36.1 + - - -
126A LYS* 3.0 17.2 + - + +
127A VAL* 3.1 9.2 + - - +
129A GLY* 1.3 76.5 - - - +
131A VAL* 1.3 64.2 + - - +
133A GLU* 3.0 38.5 + - - +
134A ILE* 2.8 40.2 + - - +
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Residues in contact with VAL 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ILE* 4.6 2.2 - - + -
83A LEU* 4.0 23.6 - - + -
110A LEU* 3.9 32.8 - - + +
113A VAL* 3.9 21.1 - - + -
114A LEU* 4.2 14.1 - - + -
127A VAL* 2.9 19.6 + - + +
128A LYS 3.5 6.3 - - - +
130A ARG* 1.3 75.0 - - - +
132A ILE* 1.3 64.7 + - - +
134A ILE* 3.2 9.0 + - - +
135A LEU* 2.9 41.1 + - + +
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Residues in contact with ILE 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A LEU* 3.9 20.4 - - + -
128A LYS* 2.9 21.7 + - + +
129A GLY* 3.5 10.8 - - - +
131A VAL* 1.3 78.0 - - - +
133A GLU* 1.3 61.9 + - - +
135A LEU* 3.3 8.4 + - - +
136A PHE* 3.2 22.3 + - - +
152A TYR* 4.3 1.2 - - + -
160A ILE 4.2 10.5 - - - +
161A ILE* 3.6 46.4 - - + -
163A GLN 5.3 0.9 - - - +
165A PRO* 4.2 18.4 - - + -
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Residues in contact with GLU 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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87A GLU* 4.9 2.6 - - - +
129A GLY 2.8 11.9 + - - +
130A ARG* 3.0 49.1 + - - +
132A ILE* 1.3 78.9 - - - +
134A ILE* 1.3 63.8 + - + +
135A LEU 3.3 0.2 + - - -
136A PHE* 3.4 2.4 + - - +
137A SER* 3.1 26.1 + - - -
165A PRO* 3.9 21.6 - - + +
166A LYS 5.5 7.8 - - - +
167A LEU* 4.8 12.3 - - - +
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Residues in contact with ILE 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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83A LEU* 3.7 41.1 - - + +
86A LEU* 4.7 7.4 - - + -
87A GLU* 3.9 25.6 - - + +
110A LEU* 5.2 4.9 - - + -
130A ARG* 2.8 40.1 + - - +
131A VAL* 3.6 5.4 - - - +
133A GLU* 1.3 77.1 - - + +
135A LEU* 1.3 60.1 + - - +
137A SER* 2.6 23.9 + - - +
138A TRP* 3.2 43.6 + - + +
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Residues in contact with LEU 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LEU* 4.5 11.2 - - + -
110A LEU* 3.9 23.1 - - + -
111A ILE* 4.7 9.9 - - + -
114A LEU* 4.5 4.0 - - + -
131A VAL* 2.9 38.3 + - + +
132A ILE* 3.7 6.5 - - - +
134A ILE* 1.3 73.5 - - - +
136A PHE* 1.3 66.0 + - - +
138A TRP* 3.2 21.1 + - + +
139A THR* 3.1 23.9 + - - +
148A ILE* 4.5 7.1 - - + +
151A ALA* 5.9 5.6 - - + -
152A TYR* 4.0 15.9 - - + +
155A LEU* 3.8 29.2 - - + -
161A ILE* 5.0 0.7 - - + -
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Residues in contact with PHE 136 (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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132A ILE 3.2 10.6 + - - +
133A GLU 3.9 1.3 - - - +
135A LEU* 1.3 75.3 - - - +
137A SER* 1.3 69.9 + - - +
139A THR* 2.4 33.5 + - - -
140A VAL* 3.0 30.3 + - + +
152A TYR* 3.5 39.8 - + + +
164A ASP* 3.5 28.3 - - + -
165A PRO* 3.7 26.9 - - + -
166A LYS 3.6 19.7 - - - -
167A LEU* 4.2 12.3 - - + -
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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 GLU* 3.1 16.1 + - - -
134A ILE* 2.6 24.9 + - - +
136A PHE* 1.3 79.6 - - - +
138A TRP* 1.3 64.3 + - - +
140A VAL* 3.2 7.2 + - - +
141A TRP* 2.8 63.9 + - - -
166A LYS 5.9 1.1 - - - -
167A LEU* 5.6 12.3 - - - -
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Residues in contact with TRP 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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86A LEU* 4.0 26.7 - - + -
87A GLU* 5.6 3.4 - - - +
90A MET* 3.2 37.1 - - + +
91A ASN* 6.3 0.2 - - - -
101A VAL* 3.3 31.4 - - + -
107A LEU* 4.0 14.8 - - + -
110A LEU* 4.1 12.6 - - + -
134A ILE* 3.2 31.0 + - + +
135A LEU* 3.4 22.2 - - + +
136A PHE 3.0 0.8 - - - -
137A SER* 1.3 84.4 + - - +
139A THR* 1.3 59.7 + - - +
140A VAL 3.0 2.0 - - - -
141A TRP* 4.1 8.2 - + - -
142A PHE* 2.7 60.8 + + + +
148A ILE* 3.9 26.2 - - + +
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Residues in contact with THR 139 (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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135A LEU 3.1 14.9 + - - +
136A PHE* 2.4 34.7 + - - -
138A TRP* 1.3 75.6 - - - +
140A VAL* 1.3 61.0 + - - +
142A PHE 4.9 2.0 - - - -
143A PRO* 3.8 21.4 - - - +
148A ILE* 4.0 17.5 - - + +
149A ARG* 4.5 12.2 - - + +
152A TYR* 3.4 37.4 - - + -
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Residues in contact with VAL 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 PHE* 3.3 39.9 - - + +
137A SER* 3.4 9.2 - - - +
138A TRP 3.0 0.4 - - - -
139A THR* 1.3 82.7 - - - +
141A TRP* 1.3 76.6 + - + +
142A PHE 3.3 1.1 - - - -
143A PRO* 3.6 10.3 - - - +
167A LEU* 4.6 16.8 - - + -
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Residues in contact with TRP 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A GLU* 5.1 13.0 - - + -
91A ASN* 4.0 31.9 - - - -
137A SER* 2.8 50.8 + - - +
138A TRP* 4.1 15.0 - + - -
140A VAL* 1.3 87.0 - - + +
142A PHE* 1.3 84.5 + + + +
143A PRO* 3.4 7.1 - - - +
144A GLU* 4.1 1.7 - - - +
167A LEU* 5.0 19.6 - - + +
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Residues in contact with PHE 142 (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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90A MET* 4.2 14.6 - - + -
91A ASN* 4.3 16.4 - - - -
98A HIS* 3.6 29.8 - + - -
138A TRP* 2.7 53.3 + + + +
139A THR* 4.4 1.9 - - - +
141A TRP* 1.3 104.3 - + + +
143A PRO* 1.3 56.5 - - - +
144A GLU* 2.9 24.7 - - - +
145A ASP* 2.9 40.1 + - + +
148A ILE* 5.2 2.0 - - + +
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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
------------------------------------------------------------
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