Contacts of the helix formed by residues 131 - 146 (chain A) in PDB entry 4OG2
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 LEU 131 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A VAL* 3.6 42.4 - - + -
70A LEU* 4.4 3.6 - - + -
105A GLY 4.6 4.0 - - - +
129A PRO* 3.6 4.5 - - - +
130A THR* 1.3 82.1 - - + +
132A SER* 1.3 65.7 + - - +
133A GLN* 3.9 13.5 - - + +
134A GLN* 3.0 26.8 + - + +
135A ALA* 3.0 17.5 + - - +
154A ASN* 4.3 3.6 - - - -
202A ASP* 4.3 9.4 - - - +
256A LEU* 4.0 35.7 - - + -
501A LEU* 3.4 21.1 - - + +
144B ARG* 6.3 0.4 - - - +
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Residues in contact with SER 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A LEU* 1.3 71.4 - - - +
133A GLN* 1.3 63.9 + - - +
135A ALA* 4.0 4.5 - - - -
136A PHE* 3.0 34.2 + - - -
154A ASN* 3.3 15.8 - - - +
156A ALA* 3.2 36.0 + - - +
159A ILE* 4.0 6.1 - - - +
204A PHE* 3.9 7.4 - - - -
501A LEU* 2.6 34.9 + - - -
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Residues in contact with GLN 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A GLU* 2.9 36.3 + - - +
131A LEU* 3.2 10.9 - - + +
132A SER* 1.3 78.6 - - - +
134A GLN* 1.3 63.3 + - + +
136A PHE* 3.9 7.2 + - - +
137A SER* 4.0 4.5 + - - -
201A ASN 3.4 17.5 + - - +
202A ASP* 3.7 21.1 + - - +
203A ALA* 2.8 42.7 + - - +
204A PHE 4.7 0.6 - - - +
206A LYS* 5.3 1.7 + - - -
501A LEU* 4.7 0.4 + - - -
140B PRO* 4.7 10.8 - - - +
143B GLU* 6.3 0.8 - - - +
144B ARG* 4.1 11.8 - - - +
162B ILE 5.4 5.1 + - - -
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Residues in contact with GLN 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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67A VAL* 4.5 1.9 - - - +
103A THR* 3.8 3.7 + - - -
104A ALA 3.0 26.7 + - - -
105A GLY* 3.3 11.7 - - - +
106A ASP* 3.1 28.1 + - - +
107A GLU* 4.5 6.6 - - - +
110A THR* 3.1 23.9 + - - +
129A PRO* 3.9 9.2 - - + -
130A THR* 4.0 11.4 + - - -
131A LEU* 3.0 44.4 + - + +
133A GLN* 1.3 81.2 - - + +
135A ALA* 1.3 60.5 + - - +
137A SER* 3.2 4.7 + - - -
138A ALA* 2.9 30.9 + - - +
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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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129A PRO* 3.5 7.4 - - + +
131A LEU 3.0 9.6 + - - +
132A SER* 3.1 8.0 + - - +
134A GLN* 1.3 78.4 - - - +
136A PHE* 1.3 58.3 + - - +
139A ASN* 2.8 56.6 + - - +
140A PRO* 3.6 0.3 - - - +
154A ASN* 3.6 27.4 - - - +
159A ILE* 3.7 11.4 - - + -
162A ILE* 3.8 1.8 - - - +
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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 SER 3.0 28.7 + - - +
133A GLN* 4.4 3.8 - - - +
134A GLN 3.3 0.2 - - - -
135A ALA* 1.3 76.1 - - - +
137A SER* 1.3 59.2 + - - +
140A PRO* 3.4 17.8 - - - +
156A ALA* 3.8 19.1 - - + -
157A LYS 3.3 23.1 - - - -
158A GLY* 3.9 20.2 - - - -
159A ILE* 3.7 21.5 - - + -
162A ILE* 3.8 17.6 - - + +
203A ALA* 4.0 19.5 - - + -
136B PHE* 4.0 16.2 - - + +
137B SER* 4.5 0.7 - - - -
140B PRO* 6.5 0.7 - - + -
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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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107A GLU* 3.6 28.7 - - - +
111A ILE* 3.4 18.6 - - - +
133A GLN 4.0 2.8 + - - -
134A GLN 3.2 7.4 + - - -
135A ALA 3.1 0.2 - - - -
136A PHE* 1.3 80.8 - - - +
138A ALA* 1.3 61.2 + - - +
140A PRO* 3.5 6.1 - - - +
141A ILE* 4.5 1.7 - - - +
136B PHE 4.2 0.7 - - - -
137B SER* 2.6 53.2 + - - +
140B PRO* 4.4 8.9 - - - +
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Residues in contact with ALA 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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107A GLU 5.0 0.2 - - - +
110A THR* 3.4 36.8 - - + -
111A ILE* 4.0 20.2 - - + +
114A PHE* 3.6 17.8 - - + -
134A GLN 2.9 10.2 + - - +
137A SER* 1.3 75.1 - - - +
139A ASN* 1.3 66.7 + - - +
140A PRO 3.2 2.9 - - - -
141A ILE* 2.9 23.2 + - - +
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Residues in contact with ASN 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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114A PHE* 3.3 26.0 - - - -
129A PRO* 3.7 5.4 - - - +
135A ALA* 2.8 45.9 + - - +
138A ALA* 1.3 71.4 - - - +
140A PRO* 1.4 63.9 - - + +
142A ALA* 3.0 7.0 + - - +
143A GLU* 2.9 20.8 + - - +
149A VAL* 4.0 16.2 - - + +
154A ASN* 4.7 1.8 - - - +
159A ILE* 4.6 4.0 - - - +
162A ILE* 4.0 13.2 - - + +
166A VAL* 3.5 35.1 - - + +
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Residues in contact with PRO 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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135A ALA 3.6 0.4 - - - +
136A PHE 3.4 26.5 - - - +
137A SER 3.5 7.0 - - - +
138A ALA 3.3 3.8 - - - -
139A ASN* 1.4 93.0 - - + +
141A ILE* 1.3 55.9 + - - +
143A GLU* 3.6 10.1 - - + +
144A ARG* 2.9 30.7 + - - +
162A ILE* 3.9 16.4 - - + -
107B GLU* 3.7 33.1 - - + +
133B GLN* 4.6 8.5 - - - +
136B PHE* 6.1 1.3 - - + -
137B SER* 4.6 4.5 - - - +
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Residues in contact with ILE 141 (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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111A ILE* 4.3 14.1 - - + -
114A PHE* 4.7 7.9 - - + -
115A GLN* 4.0 30.1 - - + +
118A ILE* 4.5 13.5 - - + -
137A SER 4.5 1.8 - - - +
138A ALA* 2.9 20.6 + - - +
140A PRO* 1.3 78.5 - - - +
142A ALA* 1.3 62.4 + - - +
144A ARG* 3.4 5.5 + - - +
145A ALA* 3.1 23.4 + - + +
107B GLU* 4.3 4.5 - - + +
108B ALA* 3.8 39.9 - - + +
111B ILE* 3.9 17.0 - - + -
137B SER* 4.9 0.4 - - - +
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Residues in contact with ALA 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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114A PHE* 4.3 12.6 - - + -
118A ILE* 4.2 13.9 - - + -
126A ILE* 4.7 1.6 - - + -
138A ALA 3.7 1.0 + - - -
139A ASN 3.0 5.8 + - - +
141A ILE* 1.3 77.6 - - - +
143A GLU* 1.3 66.9 + - - +
145A ALA* 3.2 1.4 + - - -
146A LYS 2.9 19.1 + - - -
147A VAL* 3.0 26.1 + - + +
149A VAL* 3.4 33.2 - - + -
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Residues in contact with GLU 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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139A ASN 2.9 13.4 + - - +
140A PRO* 3.6 13.0 - - + +
141A ILE 3.3 0.2 - - - -
142A ALA* 1.3 77.3 - - - +
144A ARG* 1.3 62.8 + - - +
146A LYS* 3.1 19.2 + - - +
162A ILE* 4.3 7.9 - - + +
163A GLY* 3.2 14.5 - - - -
164A ASP* 2.9 28.8 + - - +
165A TYR* 2.8 40.2 + - - +
166A VAL* 4.0 6.0 + - + +
133B GLN* 6.4 0.2 - - - +
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Residues in contact with ARG 144 (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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140A PRO 2.9 17.9 + - - +
141A ILE* 3.8 5.4 - - - +
143A GLU* 1.3 77.5 - - - +
145A ALA* 1.3 60.4 + - - +
146A LYS* 3.4 14.1 + - - +
105B GLY 3.8 15.4 + - - -
106B ASP* 3.6 32.8 - - + +
107B GLU* 2.9 41.5 + - - +
131B LEU* 6.3 0.2 - - - +
133B GLN* 4.0 15.0 - - - +
134B GLN* 5.7 0.6 - - - +
201B ASN* 5.7 6.4 + - - +
232B THR* 6.3 1.6 - - - +
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Residues in contact with ALA 145 (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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118A ILE* 4.4 17.5 - - + -
141A ILE* 3.1 18.5 + - + +
142A ALA 3.2 4.0 + - - +
144A ARG* 1.3 75.0 - - - +
146A LYS* 1.3 70.2 + - - +
147A VAL* 3.7 18.8 - - + +
364A ARG* 5.1 3.6 + - - -
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Residues in contact with LYS 146 (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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142A ALA 2.9 5.2 + - - -
143A GLU 3.1 11.3 + - - +
144A ARG 4.2 10.0 + - - +
145A ALA* 1.3 80.1 - - - +
147A VAL* 1.3 60.3 + - - +
165A TYR* 3.5 44.5 - - + +
361A PRO 4.8 1.9 - - - +
364A ARG* 3.4 22.2 - - - +
365A THR* 4.1 8.9 + - - +
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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