Contacts of the helix formed by residues 151 - 165 (chain A) in PDB entry 1OFV
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 151 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A GLY* 4.8 4.7 - - - +
148A GLN* 3.1 34.5 + - + +
149A PRO 3.1 1.0 - - - -
150A ASP* 1.3 86.9 - - + +
152A THR* 1.3 66.4 - - - +
153A LYS 3.4 1.7 + - - -
154A ASN* 3.5 10.3 + - + +
155A ARG* 3.1 59.8 + - + +
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Residues in contact with THR 152 (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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17A ILE* 5.1 4.3 - - + -
143A ILE* 3.7 30.9 - - + +
144A ASP 4.6 0.5 + - - -
145A GLU* 2.3 34.3 + - - +
148A GLN 3.7 7.9 + - - -
149A PRO 3.3 9.2 + - - -
151A LEU* 1.3 78.1 - - - +
153A LYS* 1.3 67.0 + - - +
155A ARG* 3.0 4.4 + - - +
156A ILE* 2.9 45.2 + - + +
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Residues in contact with LYS 153 (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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149A PRO 4.7 1.4 + - - -
150A ASP 5.0 3.5 + - - +
151A LEU 3.4 0.8 - - - -
152A THR* 1.3 80.9 - - - +
154A ASN* 1.3 59.8 + - + +
156A ILE* 3.3 6.6 + - - +
157A LYS* 3.0 64.1 + - + +
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Residues in contact with ASN 154 (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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120A TRP* 6.1 0.2 - - - -
150A ASP 5.5 1.7 + - - +
151A LEU* 3.5 10.9 + - + +
152A THR 3.2 0.2 - - - -
153A LYS* 1.3 81.7 - - + +
155A ARG* 1.3 64.5 + - + +
157A LYS* 3.8 8.9 - - - +
158A THR* 2.9 49.8 + - - -
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Residues in contact with ARG 155 (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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120A TRP* 3.7 28.6 - - + +
123A GLU 5.0 1.0 + - - -
124A GLY* 4.2 4.2 + - - -
125A TYR* 3.1 45.7 + - - -
141A LEU* 4.0 5.1 - - + +
142A ALA 4.0 4.0 + - - -
143A ILE* 4.0 19.5 - - + +
144A ASP 4.1 11.3 - - - +
148A GLN* 2.9 45.0 + - - +
151A LEU* 3.1 41.9 + - + +
152A THR* 3.0 7.6 + - - +
154A ASN* 1.3 81.9 - - + +
156A ILE* 1.3 63.6 + - - +
159A TRP* 3.0 27.5 + - - +
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Residues in contact with ILE 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ILE* 4.1 20.4 - - + -
20A SER* 3.8 23.6 - - - +
21A ILE* 4.1 23.8 - - + +
24A GLU* 3.8 22.0 - - + -
141A LEU* 3.9 22.0 - - + -
143A ILE* 4.4 3.1 - - + -
152A THR* 2.9 39.3 + - + +
153A LYS* 3.7 9.0 - - - +
155A ARG* 1.3 74.5 - - - +
157A LYS* 1.3 62.7 + - - +
159A TRP* 3.2 1.7 + - - +
160A VAL* 2.8 32.4 + - + +
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Residues in contact with LYS 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A GLU* 3.6 42.4 + - + +
153A LYS* 3.0 56.7 + - + +
154A ASN* 4.0 9.6 - - - +
156A ILE* 1.3 75.5 - - + +
158A THR* 1.3 62.8 + - - +
160A VAL* 4.1 1.2 - - - +
161A SER* 3.1 23.7 + - - -
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Residues in contact with THR 158 (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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120A TRP* 3.8 20.0 - - + -
154A ASN* 2.9 37.6 + - - -
157A LYS* 1.3 73.3 - - - +
159A TRP* 1.3 64.4 + - - +
161A SER* 3.2 8.0 + - - -
162A GLN* 3.0 47.5 + - - +
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Residues in contact with TRP 159 (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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21A ILE* 3.7 30.3 - - + -
51A ILE* 4.0 17.0 - - + -
84A ALA* 3.9 11.7 - - + -
85A TYR 3.2 28.5 - - - -
86A PHE* 4.3 1.8 - - + -
118A GLY* 2.8 32.5 + - - -
119A TYR 4.8 0.9 - - - -
120A TRP* 3.7 28.0 - + + -
141A LEU* 3.7 32.7 - - + +
155A ARG 3.0 19.2 + - - +
156A ILE 3.6 1.6 - - - +
158A THR* 1.3 76.2 - - - +
160A VAL* 1.3 76.6 + - + +
162A GLN* 3.1 10.3 + - + +
163A LEU* 2.9 51.5 + - + +
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Residues in contact with VAL 160 (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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21A ILE* 4.0 18.4 - - + -
24A GLU* 3.8 38.4 - - + +
25A PHE* 3.8 40.2 - - + -
156A ILE* 2.8 24.3 + - + +
157A LYS 4.1 2.2 - - - +
159A TRP* 1.3 80.5 - - + +
161A SER* 1.3 65.3 + - - +
163A LEU* 2.9 7.3 + - - +
164A LYS* 2.9 31.9 + - + +
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Residues in contact with SER 161 (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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157A LYS 3.1 13.8 + - - -
158A THR* 3.4 11.2 - - - -
159A TRP 3.1 0.2 - - - -
160A VAL* 1.3 80.1 - - - +
162A GLN* 1.3 60.3 + - - +
164A LYS* 3.6 23.1 - - - +
165A SER* 3.9 6.4 + - - -
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Residues in contact with GLN 162 (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 GLY* 6.2 4.0 - - - -
119A TYR 4.5 8.1 - - - +
120A TRP* 3.9 19.2 - - - -
121A PRO* 5.4 2.3 - - - +
158A THR* 3.0 37.7 + - - +
159A TRP* 3.6 10.3 - - + +
161A SER* 1.3 74.7 - - - +
163A LEU* 1.3 65.3 + - - +
165A SER* 3.4 17.3 + - - -
166A GLU* 4.2 7.6 + - - +
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Residues in contact with LEU 163 (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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25A PHE* 3.7 26.5 - - + -
51A ILE* 4.2 2.5 - - + -
84A ALA* 3.9 22.9 - - + -
117A VAL* 4.1 18.2 - - + -
118A GLY* 4.2 11.9 - - - +
159A TRP* 2.9 54.4 + - + +
160A VAL 3.3 8.5 - - - +
162A GLN* 1.3 78.0 - - - +
164A LYS* 1.3 67.3 + - - +
166A GLU* 2.9 20.2 + - + +
167A PHE* 3.1 25.4 + - + +
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Residues in contact with LYS 164 (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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24A GLU* 3.4 21.7 + - - -
25A PHE* 3.8 40.8 + - + +
160A VAL* 2.9 22.5 + - + +
161A SER* 3.6 16.5 - - - +
163A LEU* 1.3 74.4 - - - +
165A SER* 1.3 63.0 + - - +
167A PHE 3.1 6.9 + - - -
168A GLY 3.3 0.2 + - - -
169A LEU* 2.9 52.0 + - + +
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Residues in contact with SER 165 (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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161A SER 3.9 8.1 + - - -
162A GLN* 3.4 14.8 + - - -
164A LYS* 1.3 75.8 - - - +
166A GLU* 1.3 58.4 + - - +
168A GLY* 3.2 18.4 + - - -
169A LEU* 3.9 8.2 + - - +
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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