Contacts of the strand formed by residues 135 - 140 (chain A) in PDB entry 1P01
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 ALA 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A GLY 3.7 1.2 + - - -
134A ALA* 1.3 74.0 - - - +
136A VAL* 1.3 64.8 + - - +
137A CYS* 6.4 0.9 - - - -
159A CYS* 6.4 0.7 - - + -
160A GLY 3.2 12.8 - - - +
161A THR* 4.1 7.2 - - + +
201A THR* 4.0 17.5 - - - +
202A SER 5.5 0.3 + - - -
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Residues in contact with VAL 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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135A ALA* 1.3 76.3 - - - +
137A CYS* 1.3 71.2 - - - +
159A CYS* 3.3 1.6 - - - +
160A GLY 2.8 39.9 + - - +
161A THR 4.2 7.0 - - - -
162A ILE* 3.7 29.6 - - + -
190A ALA* 4.7 0.7 - - - +
199A TRP* 3.8 29.4 - - + -
200A ILE 3.4 23.1 - - - +
201A THR* 4.3 5.6 - - + +
210A GLN* 4.0 21.1 - - + -
228A PHE* 5.4 0.2 - - + -
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Residues in contact with CYS 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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135A ALA* 6.0 0.9 - - - -
136A VAL* 1.3 77.7 - - - +
138A ARG* 1.3 63.9 + - - +
157A TYR* 3.4 32.5 - - + +
158A GLN 3.1 6.3 - - - +
159A CYS* 2.0 46.9 - - - -
190A ALA* 5.3 0.2 - - - -
199A TRP* 3.3 6.3 - - - +
200A ILE* 2.8 37.2 + - + +
202A SER* 5.4 10.3 - - - -
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Residues in contact with ARG 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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137A CYS* 1.3 77.8 - - - +
139A SER* 1.3 63.9 + - - +
140A GLY* 3.1 30.9 - - - +
143A THR* 2.8 21.4 + - - -
156A GLY 3.3 8.9 + - - +
157A TYR* 3.2 6.8 - - - -
158A GLN* 2.7 52.0 + - - +
190A ALA* 3.9 11.7 - - + -
191A CYS 2.9 23.7 + - - -
192A MET* 4.0 1.8 - - - -
194A ASP* 3.1 27.5 + - - +
197A GLY 6.3 0.4 - - - -
198A SER 3.1 13.2 - - - +
199A TRP* 3.6 37.4 - - + +
200A ILE* 5.5 0.7 - - - -
213A MET* 3.9 18.7 - - - +
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Residues in contact with SER 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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19A GLY* 3.6 18.0 - - - -
118A VAL* 3.5 27.9 - - - +
119A ALA* 2.8 25.2 + - - +
138A ARG* 1.3 82.6 + - - +
140A GLY* 1.3 59.1 + - - +
156A GLY 3.5 8.8 + - - -
157A TYR* 3.9 3.8 - - - -
194A ASP 4.8 0.2 - - - +
197A GLY* 3.4 24.4 - - - -
198A SER* 2.9 9.4 + - - -
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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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19A GLY 3.3 13.4 + - - -
43A SER* 3.4 11.2 - - - -
138A ARG* 3.1 7.6 - - - +
139A SER* 1.3 77.4 + - - +
141A ARG* 1.3 61.4 + - - -
142A THR 3.2 3.4 - - - -
156A GLY* 3.0 29.1 + - - -
194A ASP* 3.3 13.0 - - - -
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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