Contacts of the helix formed by residues 124 - 136 (chain A) in PDB entry 2A0M
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 GLN 124 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A PHE* 3.3 34.1 - - + +
101A LEU* 3.9 10.5 - - + +
117A VAL* 3.7 10.2 + - - +
119A GLY* 3.1 23.8 + - - +
121A GLY 3.1 15.6 + - - +
122A ASN 3.1 1.0 - - - -
123A ASP* 1.3 79.2 - - - +
125A SER* 1.3 63.3 + - - +
126A ALA 3.2 0.2 - - - -
127A PRO* 3.2 13.4 - - - +
128A ASN* 3.2 24.8 + - - +
278A ASP* 3.7 19.7 - - - +
279A MET 3.2 23.2 + - - -
280A SER* 2.9 24.7 + - - +
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Residues in contact with SER 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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122A ASN* 3.1 24.1 + - - -
123A ASP 3.1 1.6 - - - -
124A GLN* 1.3 78.4 - - - +
126A ALA* 1.3 56.6 + - - +
128A ASN* 3.9 2.7 - - - -
129A GLY* 3.0 23.4 + - - -
165A PRO* 4.1 4.7 - - - -
166A PHE* 3.7 26.0 - - - -
169A LEU* 3.9 5.3 - - - +
232A PHE* 3.5 8.4 - - - -
234A SER* 3.2 11.2 + - - -
278A ASP* 2.8 24.7 + - - -
280A SER* 3.9 2.4 + - - -
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Residues in contact with ALA 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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123A ASP 3.4 7.0 + - - +
125A SER* 1.3 74.4 - - - +
127A PRO* 1.3 76.0 - - + +
129A GLY* 3.1 3.3 + - - -
130A ARG* 2.9 31.9 + - - +
160A VAL* 6.5 0.2 - - + -
165A PRO* 3.7 14.5 - - + +
168A GLN* 3.7 37.2 - - + +
169A LEU* 3.6 12.8 - - - +
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Residues in contact with PRO 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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98A HIS* 3.2 51.4 - - + +
101A LEU* 4.1 6.5 - - + -
102A GLU* 3.5 22.4 - - + +
123A ASP 3.3 9.6 - - - +
124A GLN* 3.2 16.4 - - - +
126A ALA* 1.3 94.3 - - + +
128A ASN* 1.3 59.7 + - - +
130A ARG* 3.2 20.9 + - - +
131A ALA* 3.0 20.8 + - - +
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Residues in contact with ASN 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LEU* 3.4 13.2 - - - +
105A VAL* 3.3 23.6 - - - +
117A VAL* 3.8 14.2 - - - +
124A GLN* 3.2 18.4 + - - +
125A SER 3.8 0.4 - - - +
126A ALA 3.2 0.2 - - - -
127A PRO* 1.3 75.3 - - - +
129A GLY* 1.3 62.6 + - - +
131A ALA* 3.3 8.2 + - - +
132A MET* 3.2 24.9 + - - +
232A PHE* 3.6 20.0 - - + -
276A MET* 3.6 17.8 - - + +
278A ASP* 3.0 37.2 + - - +
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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
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125A SER 3.0 16.9 + - - -
126A ALA 3.1 3.6 + - - -
128A ASN* 1.3 72.4 - - - +
130A ARG* 1.3 60.9 + - - +
132A MET* 3.2 7.3 + - - +
133A LEU* 3.0 31.4 + - - +
140A VAL* 5.4 0.3 - - - +
142A VAL* 5.8 2.0 - - - -
169A LEU* 3.8 21.5 - - - -
232A PHE* 3.7 12.0 - - - -
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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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98A HIS* 4.6 10.5 + - - +
102A GLU* 2.8 38.2 + - - +
126A ALA* 2.9 19.0 + - - +
127A PRO* 3.6 33.3 - - - +
129A GLY* 1.3 76.0 - - - +
131A ALA* 1.3 61.8 + - - +
133A LEU* 3.3 8.8 + - - +
134A ARG* 3.1 24.1 + - - +
168A GLN* 3.4 30.9 - - - +
169A LEU* 3.9 6.4 - - + +
172A GLU* 3.8 25.6 + - - +
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Residues in contact with ALA 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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102A GLU* 3.5 29.1 - - - +
105A VAL* 3.7 22.7 - - + -
106A PHE* 3.8 17.0 - - - +
109A LEU* 4.0 2.5 - - - -
127A PRO 3.0 11.7 + - - +
128A ASN 3.5 9.2 - - - +
129A GLY 3.3 0.2 - - - -
130A ARG* 1.3 75.6 - - - +
132A MET* 1.3 58.4 + - - +
134A ARG* 3.4 2.6 + - - -
135A ALA* 3.0 29.8 + - - +
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Residues in contact with MET 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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109A LEU* 3.7 23.8 - - + -
128A ASN 3.2 13.1 + - - +
129A GLY* 3.2 9.6 + - - +
131A ALA* 1.3 78.2 - - - +
133A LEU* 1.3 57.2 + - - +
135A ALA 3.2 0.2 + - - -
136A PHE* 2.9 48.6 + - + -
140A VAL* 3.3 20.8 - - + +
230A ASN 3.2 35.0 - - - +
231A THR 3.8 3.6 - - - +
232A PHE* 3.8 24.0 - - + +
275A MET* 4.2 4.7 - - + -
276A MET* 3.8 26.5 - - + -
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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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129A GLY 3.0 22.7 + - - +
130A ARG* 3.3 10.7 + - - +
132A MET* 1.3 75.7 - - - +
134A ARG* 1.3 61.0 + - - +
136A PHE 3.8 0.6 - - - +
137A PRO* 3.4 24.3 - - - +
138A GLY 4.5 2.6 + - - +
139A ASP 6.1 0.2 - - - +
140A VAL* 3.8 30.1 - - + -
169A LEU* 4.6 7.2 - - + +
172A GLU* 3.5 42.6 - - + +
174A SER* 4.1 21.3 + - - +
175A PHE* 3.9 25.1 - - + -
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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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102A GLU* 5.8 1.8 - - - +
106A PHE* 3.6 26.2 - - + -
130A ARG 3.1 16.2 + - - +
131A ALA* 3.8 4.7 - - - +
133A LEU* 1.3 76.4 - - - +
135A ALA* 1.3 62.5 + - - +
136A PHE 3.6 0.2 + - - -
137A PRO* 3.8 13.3 - - - +
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Residues in contact with ALA 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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106A PHE* 3.7 16.5 - - + -
109A LEU* 4.0 21.3 - - + -
110A ALA* 5.2 2.2 - - - +
131A ALA 3.0 17.7 + - - +
132A MET 3.2 0.2 + - - -
134A ARG* 1.3 76.6 - - - +
136A PHE* 1.3 88.3 + - + +
137A PRO* 3.4 7.4 - - - +
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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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109A LEU* 4.3 16.8 - - + -
132A MET* 2.9 43.9 + - + +
133A LEU 3.6 3.9 - - - +
135A ALA* 1.3 97.4 - - + +
137A PRO* 1.3 68.2 - - - +
138A GLY 3.2 0.7 + - - -
139A ASP* 3.0 16.5 + - + +
140A VAL* 3.5 15.8 - - + +
230A ASN* 3.3 43.3 - - + +
275A MET* 3.9 30.3 - - + -
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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