Contacts of the helix formed by residues 114 - 130 (chain A) in PDB entry 1M4R
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 TYR 114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A ARG* 3.1 57.7 + - - +
58A MET* 3.5 36.5 - - + +
59A LEU* 4.2 14.4 - - + -
62A GLU* 4.1 22.7 - - - -
111A PHE 4.4 3.4 - - - +
112A GLN 3.5 1.6 - - - -
113A PRO* 1.3 98.2 - - + +
115A MET* 1.3 66.8 + - - +
117A GLU* 3.1 9.4 + - - +
118A VAL* 3.0 27.8 + - - +
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Residues in contact with MET 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A LEU* 3.9 14.5 - - + +
104A LEU* 3.9 17.5 - - + +
107A GLN* 3.6 18.4 - - + +
108A SER* 3.3 22.9 - - - +
110A ARG 3.0 25.6 - - - +
111A PHE* 3.2 26.0 + - + +
114A TYR* 1.3 75.7 - - - +
116A GLN* 1.3 59.1 + - - +
117A GLU 3.1 0.2 + - - -
119A VAL* 3.1 58.0 + - + +
164A ILE* 3.6 35.2 - - + -
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Residues in contact with GLN 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 SER 2.9 26.0 - - - +
109A ASP* 3.9 4.4 - - - -
110A ARG 3.5 11.1 - - - +
112A GLN* 3.4 22.3 - - - +
113A PRO* 2.8 39.1 + - + +
115A MET* 1.3 73.5 - - - +
117A GLU* 1.3 60.1 + - + +
119A VAL* 5.3 1.1 - - - -
120A PRO* 3.3 22.0 - - - +
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Residues in contact with GLU 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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51A TYR* 2.4 31.4 + - + -
52A ILE* 3.4 23.8 - - + +
55A ARG* 2.8 33.3 + - + -
113A PRO* 4.0 12.4 - - - +
114A TYR* 3.1 14.3 + - - +
116A GLN* 1.3 81.2 - - + +
118A VAL* 1.3 65.1 + - - +
120A PRO* 3.4 9.8 - - - +
121A PHE* 3.7 6.6 + - - +
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Residues in contact with VAL 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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52A ILE* 4.3 5.8 - - + -
55A ARG* 3.8 15.0 - - + +
56A THR* 3.8 43.3 - - + +
59A LEU* 3.9 23.8 - - + -
104A LEU* 5.7 0.2 - - + -
114A TYR 3.0 16.5 + - - +
117A GLU* 1.3 76.3 - - - +
119A VAL* 1.3 67.1 + - + +
121A PHE* 3.1 4.5 + - + +
122A LEU* 2.9 42.9 + - + +
167A LEU* 4.2 7.2 - - + -
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Residues in contact with VAL 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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100A LEU* 4.2 3.9 - - + +
104A LEU* 4.1 23.1 - - + +
105A PHE* 3.9 30.7 - - + -
108A SER* 5.0 8.3 - - - -
115A MET* 3.1 40.6 + - + +
116A GLN* 5.3 1.1 - - - -
118A VAL* 1.3 76.7 - - + +
120A PRO* 1.3 68.2 - - + +
122A LEU* 3.2 7.1 + - - +
123A ALA* 2.9 29.0 + - + +
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Residues in contact with PRO 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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116A GLN* 3.3 26.5 - - - +
117A GLU* 3.4 11.0 - - - +
119A VAL* 1.3 96.3 - - + +
121A PHE* 1.3 59.5 + - - +
123A ALA* 3.4 6.9 + - + +
124A ARG* 3.0 43.0 + - - +
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Residues in contact with PHE 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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46A ASN* 3.5 29.2 - - + -
47A PHE* 4.7 0.7 - + - -
52A ILE* 3.6 41.5 - - + -
56A THR* 4.0 13.2 - - - -
117A GLU 3.7 6.4 + - - +
118A VAL 3.1 9.6 + - - +
120A PRO* 1.3 80.0 - - - +
122A LEU* 1.3 84.7 + - + +
124A ARG* 3.1 38.8 + - + +
125A LEU* 3.2 35.0 + - + +
171A PHE* 4.0 27.6 - + - -
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Residues in contact with LEU 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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56A THR* 5.6 4.3 - - + +
96A LEU* 3.8 23.2 - - + +
100A LEU* 3.9 9.4 - - + +
104A LEU* 3.6 27.1 - - + -
118A VAL* 2.9 36.6 + - + +
119A VAL 3.8 2.9 - - - +
121A PHE* 1.3 94.7 - - + +
123A ALA* 1.3 59.0 + - - +
125A LEU* 3.1 16.9 + - + +
126A SER* 3.0 26.9 + - - -
167A LEU* 4.2 15.5 - - + -
170A LEU* 4.8 7.6 - - + -
171A PHE* 5.7 6.1 - - + -
174A LEU* 4.6 7.4 - - + -
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Residues in contact with ALA 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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100A LEU* 3.8 21.0 - - + +
105A PHE* 5.2 7.9 - - + -
119A VAL* 2.9 21.0 + - + +
120A PRO* 3.7 8.7 - - + +
122A LEU* 1.3 76.0 - - - +
124A ARG* 1.3 57.8 + - + +
126A SER* 3.2 3.3 + - - -
127A ASN* 2.8 28.1 + - - +
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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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52A ILE* 5.9 1.0 - - - +
120A PRO* 3.0 39.0 + - - +
121A PHE* 3.1 32.6 + - + +
123A ALA* 1.3 77.6 - - + +
125A LEU* 1.3 64.3 + - + +
127A ASN* 3.2 8.7 + - - +
128A ARG* 3.0 22.2 + - - +
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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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42A LEU* 4.1 19.8 - - + +
46A ASN* 3.4 38.1 - - + +
47A PHE* 3.9 19.1 - - + -
96A LEU* 4.1 9.6 - - + -
121A PHE* 3.2 37.3 + - + +
122A LEU* 3.1 26.1 + - + +
124A ARG* 1.3 75.5 - - + +
126A SER* 1.3 66.9 + - - +
128A ARG* 3.1 8.0 + - + +
129A LEU* 3.0 25.7 + - - +
174A LEU* 4.4 8.7 - - + -
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Residues in contact with SER 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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93A LYS* 6.2 0.7 - - - -
96A LEU* 3.6 9.8 - - - +
97A ASN* 2.5 33.3 + - - +
100A LEU* 3.5 24.0 - - - +
122A LEU 3.0 6.2 + - - -
123A ALA* 3.4 9.0 - - - -
125A LEU* 1.3 78.2 - - - +
127A ASN* 1.3 57.1 + - - +
129A LEU* 3.1 6.5 + - - +
130A SER* 2.8 27.8 + - - -
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Residues in contact with ASN 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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123A ALA 2.8 14.4 + - - +
124A ARG* 3.5 11.8 + - - +
126A SER* 1.3 77.8 - - - +
128A ARG* 1.3 58.9 + - - +
130A SER* 2.6 34.9 + - - -
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Residues in contact with ARG 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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39A HIS* 4.8 10.9 + - - -
41A ARG* 2.8 45.7 + - - +
42A LEU* 3.5 22.7 - - + +
43A ASP* 3.9 11.1 - - - +
46A ASN* 5.3 4.8 - - - +
124A ARG 3.0 12.6 + - - +
125A LEU* 3.1 12.1 + - + +
127A ASN* 1.3 79.3 - - - +
129A LEU* 1.3 61.0 + - - +
130A SER* 3.5 2.9 + - - +
132A CYS* 5.6 0.7 - - - +
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Residues in contact with LEU 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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40A CYS* 4.0 9.2 - - + -
41A ARG 3.8 25.1 - - - +
42A LEU* 3.9 20.9 - - + -
89A CYS* 3.7 26.9 - - - -
93A LYS* 3.6 37.6 + - + +
96A LEU* 4.4 9.0 - - + -
125A LEU 3.0 16.4 + - - +
126A SER 3.1 6.0 + - - +
128A ARG* 1.3 75.5 - - - +
130A SER* 1.3 66.3 + - - +
131A THR 3.2 0.7 + - - -
132A CYS* 2.9 33.3 + - - +
174A LEU* 4.4 11.9 - - + -
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Residues in contact with SER 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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38A SER* 5.2 1.6 + - - -
93A LYS* 4.4 4.7 - - - +
97A ASN* 6.0 0.2 - - - +
126A SER 2.8 12.7 + - - -
127A ASN* 2.6 32.3 + - - -
128A ARG 3.2 3.0 + - - +
129A LEU* 1.3 77.7 - - - +
131A THR* 1.3 70.9 + - - +
132A CYS* 3.2 3.6 + - - +
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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
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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