Contacts of the strand formed by residues 212 - 219 (chain A) in PDB entry 1OPO
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 GLY 212 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A VAL* 3.6 8.7 - - - +
109A VAL* 2.8 24.0 + - - +
155A PHE* 3.8 10.5 - - - -
156A ASN 3.3 12.3 - - - -
157A ASP* 3.9 8.3 - - - -
159A ALA* 4.0 10.9 - - - +
210A ASP 3.5 2.6 - - - -
211A PHE* 1.3 81.3 - - - +
213A ARG* 1.3 61.1 + - - +
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Residues in contact with ARG 213 (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 ASP* 3.2 33.2 + - + -
107A TRP 3.3 12.1 - - - +
108A VAL* 3.7 22.3 - - - +
109A VAL 4.5 0.2 - - - +
155A PHE* 3.3 7.9 - - - -
156A ASN* 2.7 43.8 + - + +
158A ASP 4.7 0.4 + - - +
159A ALA* 2.6 37.6 + - - +
160A SER 4.8 0.2 - - - -
161A ASP 3.1 18.1 + - - -
163A PRO* 3.8 22.8 - - - +
212A GLY* 1.3 74.1 - - - +
214A ILE* 1.3 74.5 + - - +
215A VAL* 4.2 9.4 + - + +
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Residues in contact with ILE 214 (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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91A LEU* 5.3 11.0 - - + -
106A ASP* 3.1 7.6 - - - +
107A TRP* 2.8 57.9 + - + +
109A VAL* 3.8 25.1 - - + -
116A VAL* 5.4 4.7 - - + -
135A LEU* 5.5 4.5 - - + -
137A VAL* 3.8 32.5 - - + -
153A LEU* 5.2 8.7 - - + -
154A GLY 3.5 8.3 - - - +
155A PHE* 4.2 10.8 - - + -
187A LEU* 5.7 2.9 - - + -
189A ILE* 5.1 4.7 - - + -
213A ARG* 1.3 75.9 - - - +
215A VAL* 1.3 69.4 + - - +
231A LEU* 6.4 0.4 - - + -
233A ILE* 5.3 6.7 - - + -
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Residues in contact with VAL 215 (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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104A PHE* 4.1 13.7 - - + -
105A GLU 3.2 8.5 - - - +
106A ASP* 4.1 12.3 - - + -
153A LEU* 3.4 7.3 - - - +
154A GLY 2.8 42.2 + - - +
156A ASN* 6.1 1.8 - - + +
163A PRO* 5.2 0.9 - - + -
164A PRO* 4.1 22.9 - - + -
170A PHE* 3.6 29.2 - - + -
173A LEU* 4.7 7.6 - - + -
213A ARG* 4.4 12.8 - - + +
214A ILE* 1.3 85.8 - - - +
216A LEU* 1.3 68.5 + - - +
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Residues in contact with LEU 216 (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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92A SER* 5.0 2.2 - - - +
93A THR 5.3 0.9 - - - +
94A VAL* 4.3 24.7 - - + -
103A SER 3.7 0.2 - - - +
104A PHE* 3.2 5.9 - - - -
105A GLU* 2.8 55.9 + - + +
107A TRP* 3.8 17.0 - - + -
151A VAL* 4.3 15.9 - - + -
152A ALA 3.5 11.4 - - - +
153A LEU* 3.6 16.4 - - + -
215A VAL* 1.3 77.0 - - - +
217A SER* 1.3 79.2 + - - +
218A THR* 4.4 7.0 - - + -
231A LEU* 4.3 16.4 - - + -
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Residues in contact with SER 217 (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 PRO* 3.9 10.7 - - - +
103A SER 3.2 6.6 + - - -
104A PHE* 3.2 29.5 - - - -
150A ARG* 4.5 0.9 - - - +
151A VAL* 3.6 1.0 - - - -
152A ALA* 3.0 34.6 + - - +
170A PHE* 3.7 24.2 - - - +
171A TYR* 6.4 0.2 - - - -
216A LEU* 1.3 78.6 - - - +
218A THR* 1.3 67.4 + - - +
219A TYR* 4.0 10.0 - - - -
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Residues in contact with THR 218 (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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94A VAL* 4.4 8.3 - - + -
95A LYS 4.1 15.5 + - - +
97A THR* 3.1 24.5 + - - +
103A SER* 2.9 30.1 + - - -
150A ARG 3.4 12.8 - - - +
151A VAL* 4.3 14.1 - - + -
216A LEU* 4.4 15.7 - - + -
217A SER* 1.3 80.8 + - - +
219A TYR* 1.3 73.0 + - - +
221A PHE* 3.9 9.6 - - + -
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Residues in contact with TYR 219 (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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97A THR* 3.4 14.8 - - - -
99A GLY 3.4 12.1 - - - +
100A VAL* 4.6 3.1 - - - -
101A ILE 3.8 14.8 - - - +
102A PRO* 3.7 22.2 - - + -
150A ARG* 2.9 56.0 + - + +
167A LYS* 3.8 33.1 - - + +
171A TYR* 2.8 33.3 + + - -
217A SER* 4.0 14.4 - - - -
218A THR* 1.3 91.4 - - - +
220A GLY* 1.3 66.0 + - - +
221A PHE* 3.4 3.3 - - - -
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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