Contacts of the helix formed by residues 122 - 137 (chain A) in PDB entry 3OM0
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 SER 122 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A GLU* 3.7 11.0 - - - -
120A TYR 3.4 3.5 + - - -
121A PRO* 1.3 77.6 - - - +
123A ASN* 1.3 65.9 + - - +
124A GLU* 3.5 7.8 + - - +
125A ASP* 3.0 34.3 + - - +
126A VAL* 3.0 20.8 + - - +
350A GLN* 3.7 38.7 + - - +
351A ARG* 5.8 2.0 + - - +
354A TYR* 4.4 0.6 + - - -
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Residues in contact with ASN 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A PRO* 5.4 1.0 - - - +
104A GLU* 2.9 44.5 + - - +
105A GLU 5.1 0.2 + - - -
106A THR* 3.1 28.6 + - - +
121A PRO 3.8 0.9 + - - +
122A SER* 1.3 72.2 - - - +
124A GLU* 1.3 62.6 + - - +
126A VAL* 3.2 9.0 + - - +
127A SER* 3.0 24.6 + - - -
153A LEU 4.7 2.1 + - - +
154A ARG* 3.3 50.4 + - - +
155A LEU* 5.1 0.2 - - - +
156A GLU* 6.3 1.3 - - + -
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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
----------------------------------------------------------
104A GLU* 4.5 0.8 + - - -
122A SER* 3.2 8.3 + - - +
123A ASN* 1.3 77.7 - - - +
125A ASP* 1.3 62.0 + - - +
127A SER* 3.2 7.4 + - - -
128A LEU* 2.9 54.4 + - + +
157A GLU* 4.7 21.5 - - + +
348A LYS* 4.3 15.9 + - - -
350A GLN* 5.1 5.5 + - - +
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Residues in contact with ASP 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A PRO* 4.6 1.8 - - + -
122A SER* 3.0 27.8 + - - +
124A GLU* 1.3 83.5 - - - +
126A VAL* 1.3 56.7 + - - +
128A LEU* 3.3 9.9 + - - +
129A ALA* 2.9 30.9 + - - +
351A ARG 3.9 8.3 - - - +
354A TYR* 2.9 40.0 + - - +
356A LEU* 5.5 1.3 - - - -
372A TRP* 3.5 27.6 - - + -
374A SER* 4.2 5.7 - - - +
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Residues in contact with VAL 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A TYR* 5.1 7.9 - - + +
121A PRO* 4.2 16.2 - - + +
122A SER 3.0 14.9 + - - +
123A ASN* 3.2 10.3 + - - +
125A ASP* 1.3 73.7 - - - +
127A SER* 1.3 63.3 + - - +
129A ALA* 3.2 6.2 + - - +
130A VAL* 3.0 25.6 + - + +
154A ARG* 5.3 8.5 - - + -
155A LEU* 4.3 9.2 - - + -
226A THR* 4.1 37.0 - - + +
228A MET* 4.1 22.7 - - + -
248A PHE* 5.4 1.6 - - + -
356A LEU* 5.5 0.9 - - - -
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Residues in contact with SER 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ASN 3.0 14.2 + - - -
124A GLU* 3.4 7.8 - - - -
126A VAL* 1.3 74.9 - - - +
128A LEU* 1.3 59.0 + - - +
130A VAL* 3.4 5.5 + - - +
131A SER* 2.9 33.3 + - - -
154A ARG 3.7 1.2 + - - -
155A LEU* 3.4 41.0 - - - +
157A GLU* 3.6 25.7 - - - +
158A LEU* 3.7 10.5 + - - +
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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
----------------------------------------------------------
124A GLU* 2.9 44.1 + - + +
125A ASP* 3.7 15.3 - - - +
127A SER* 1.3 77.5 - - - +
129A ALA* 1.3 58.2 + - - +
131A SER* 3.3 10.1 + - - -
132A ARG* 2.9 27.4 + - - +
157A GLU* 3.9 26.5 - - + +
372A TRP* 3.8 20.4 + - + +
374A SER 6.1 0.9 - - - +
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Residues in contact with ALA 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ASP 2.9 16.4 + - - +
126A VAL* 3.2 4.9 + - - +
128A LEU* 1.3 73.7 - - - +
130A VAL* 1.3 66.2 + - - +
132A ARG* 3.2 12.1 + - - +
133A ILE* 3.2 17.2 + - - +
248A PHE* 3.6 28.3 - - + -
356A LEU* 4.1 11.9 - - + -
358A ILE* 5.2 0.5 - - - +
372A TRP* 3.7 27.7 - - + +
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Residues in contact with VAL 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A VAL* 3.0 22.1 + - + +
127A SER* 3.7 5.6 - - - +
129A ALA* 1.3 74.1 - - - +
131A SER* 1.3 63.3 + - - +
133A ILE* 3.1 6.8 + - - +
134A LEU* 3.0 22.5 + - + +
155A LEU* 5.2 3.1 - - + -
158A LEU* 3.5 24.5 - - + -
196A ILE* 4.2 20.4 - - + -
224A ILE* 4.1 28.0 - - + -
226A THR* 4.2 24.0 - - + -
248A PHE* 4.2 13.2 - - + -
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Residues in contact with SER 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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127A SER 2.9 23.9 + - - -
128A LEU* 3.5 13.6 - - - +
129A ALA 3.2 0.2 - - - -
130A VAL* 1.3 75.4 - - - +
132A ARG* 1.3 57.2 + - - +
134A LEU* 3.2 12.6 + - - +
135A LYS* 2.9 28.2 + - - +
139A TYR* 4.3 7.4 - - - -
157A GLU* 5.4 2.6 - - - +
158A LEU* 3.9 19.2 - - - +
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Residues in contact with ARG 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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128A LEU 2.9 14.0 + - - +
129A ALA 3.2 10.0 + - - +
131A SER* 1.3 73.9 - - - +
133A ILE* 1.3 65.4 + - - +
135A LYS* 3.4 26.0 + - - +
136A SER* 3.2 28.0 + - - +
358A ILE* 4.5 16.8 - - + -
371A VAL 5.0 8.0 + - - +
372A TRP* 3.9 21.8 - - + +
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Residues in contact with ILE 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 ALA 3.7 7.4 - - - +
130A VAL 3.1 7.4 + - - +
132A ARG* 1.3 75.6 - - - +
134A LEU* 1.3 63.5 + - - +
136A SER* 2.7 28.5 + - - +
137A PHE* 3.2 26.6 + - + -
224A ILE* 3.6 32.3 - - + -
246A LEU* 3.8 20.9 - - + -
247A GLY 5.0 1.8 - - - +
248A PHE* 3.7 26.2 - - + -
358A ILE* 3.8 35.7 - - + -
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Residues in contact with LEU 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A VAL* 3.0 17.8 + - + +
131A SER* 3.2 11.6 + - - +
133A ILE* 1.3 76.6 - - - +
135A LYS* 1.3 58.7 + - - +
137A PHE* 3.0 13.9 + - + +
139A TYR* 2.8 32.2 + - + -
140A PRO* 4.2 18.2 - - + +
142A ALA* 4.8 4.5 - - + -
158A LEU* 3.8 28.9 - - + -
162A PHE* 3.9 22.7 - - + -
194A THR* 3.9 20.2 - - + -
196A ILE* 4.4 6.3 - - + -
224A ILE* 3.8 20.0 - - + -
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Residues in contact with LYS 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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131A SER 2.9 12.6 + - - +
132A ARG* 3.5 33.9 - - - +
134A LEU* 1.3 75.8 - - - +
136A SER* 1.3 57.5 + - - +
138A ASN* 2.9 20.1 + - - -
139A TYR* 3.2 46.9 + - + +
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Residues in contact with SER 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ARG* 3.2 20.9 + - - +
133A ILE* 2.7 22.4 + - - +
135A LYS* 1.3 80.5 - - - +
137A PHE* 1.3 71.3 + - - +
138A ASN* 3.2 1.4 + - - +
246A LEU* 5.5 0.7 - - - +
403A GOL 5.9 0.2 - - - -
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Residues in contact with PHE 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 ILE* 3.2 22.2 + - + -
134A LEU* 3.0 15.9 + - + +
136A SER* 1.3 91.6 - - - +
138A ASN* 1.3 68.8 + - - +
139A TYR 3.3 0.2 - - - -
140A PRO* 3.5 19.5 - - + +
194A THR* 3.8 16.4 - - + -
222A LYS* 3.5 55.4 - - + +
223A TYR 5.3 0.2 - - - -
224A ILE* 3.9 21.5 - - + -
246A LEU* 3.9 19.1 - - + -
403A GOL 4.2 14.8 - - - -
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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