Contacts of the strand formed by residues 135 - 140 (chain A) in PDB entry 1OP8
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 MET 135 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A GLY 4.4 6.1 - - - +
134A THR* 1.3 77.2 - - - +
136A CYS* 1.3 64.5 + - - +
137A GLN* 4.9 5.1 + - - +
160A ILE 3.6 5.6 - - - +
161A THR* 4.5 6.5 - - - +
202A GLU* 3.3 39.4 + - - +
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Residues in contact with CYS 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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134A THR* 3.8 3.1 - - - -
135A MET* 1.3 76.0 - - - +
137A GLN* 1.3 65.5 + - - +
159A ASN* 3.4 4.0 - - - -
160A ILE* 2.6 47.2 + - + +
162A ILE* 3.6 27.4 - - + -
183A ALA* 5.2 0.2 - - - -
199A LEU* 3.8 13.0 - - + -
200A LEU 2.9 17.0 - - - +
201A CYS* 2.0 44.0 - - - -
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Residues in contact with GLN 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A TYR* 5.7 0.7 - - - +
135A MET* 4.9 4.2 + - - +
136A CYS* 1.3 87.7 + - - +
138A VAL* 1.3 68.5 + - - +
157A GLU* 3.4 33.6 + - + +
158A VAL 3.0 14.8 - - - +
159A ASN* 4.0 14.6 - - - +
160A ILE* 4.0 0.9 - - - -
198A PRO 4.2 0.3 - - - +
199A LEU* 3.9 1.6 - - - +
200A LEU* 2.8 57.8 + - + +
201A CYS* 4.9 0.3 - - - -
202A GLU 4.9 1.0 + - - -
207A GLY* 4.5 11.1 + - - -
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Residues in contact with VAL 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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16A ILE* 3.3 16.0 - - + +
137A GLN* 1.3 83.3 - - - +
139A ALA* 1.3 64.8 + - - +
157A GLU* 3.2 5.8 - - - -
158A VAL* 3.1 29.5 + - + +
160A ILE* 3.2 28.7 - - + -
190A SER* 4.4 9.9 - - - -
197A SER* 3.5 19.7 - - - +
198A PRO 3.9 9.4 - - - +
199A LEU* 4.0 7.9 - - + -
200A LEU* 5.8 0.9 - - - -
213A THR* 3.7 19.3 - - - +
228A TYR* 3.5 13.2 - - + +
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Residues in contact with ALA 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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16A ILE* 3.9 3.9 - - - +
27A ARG* 5.0 3.4 - - + -
29A TYR* 5.8 1.3 - - - +
30A MET* 3.4 23.7 - - + +
138A VAL* 1.3 74.4 - - - +
140A GLY* 1.3 58.5 + - - +
155A LEU* 3.7 18.4 - - + -
156A ARG 2.7 15.5 - - - +
157A GLU* 4.0 18.7 + - + +
194A ASP* 4.5 0.2 - - - +
197A SER* 2.5 32.5 + - - -
198A PRO 4.8 1.4 + - - -
200A LEU* 6.2 0.8 - - - +
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Residues in contact with GLY 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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16A ILE* 3.6 5.1 - - - +
30A MET* 4.6 2.2 - - - -
43A ALA* 4.9 2.0 - - - -
139A ALA* 1.3 77.7 - - - +
141A TRP* 1.3 63.2 + - - -
142A GLY 3.2 6.3 + - - +
152A SER* 5.1 0.5 - - - -
154A THR 4.3 0.5 - - - +
155A LEU* 3.3 12.7 - - - +
156A ARG* 2.7 34.1 + - - +
194A ASP* 3.1 18.4 - - - -
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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