Contacts of the strand formed by residues 134 - 140 (chain D) in PDB entry 1SA0
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 134 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4D ILE* 3.4 9.1 - - - +
5D VAL 3.2 22.3 + - - -
132D LEU* 3.6 7.8 - - - +
133D GLN* 1.3 82.6 - - - +
135D PHE* 1.3 67.7 + - - -
164D ARG* 3.9 11.9 - - - -
165D ILE 3.4 12.1 - - - -
252D LEU* 4.9 5.6 - - - -
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Residues in contact with PHE 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D ILE* 5.5 0.9 - - - -
5D VAL* 3.0 38.1 - - + +
7D ILE* 4.7 13.7 - - + -
122D VAL* 4.4 17.5 - - + -
126D SER* 4.5 4.5 - - - -
132D LEU* 3.6 29.4 - - + -
134D GLY* 1.3 79.9 - - - -
136D GLN* 1.3 63.1 + - - +
157D ILE* 3.6 24.2 - - + -
161D TYR* 3.7 34.8 - + + -
164D ARG* 4.6 4.3 - - + -
165D ILE 3.1 9.0 + - - +
166D MET* 3.2 21.9 - - + -
167D ASN* 2.9 29.0 + - - +
252D LEU* 5.4 1.8 - - - +
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Residues in contact with GLN 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D ILE* 3.6 19.1 - - + +
5D VAL 3.2 6.5 + - - +
6D HIS* 3.2 26.3 + - + -
7D ILE* 2.9 26.4 + - - +
20D PHE* 4.2 8.3 - - - -
52D TYR* 2.9 36.6 + - - -
135D PHE* 1.3 77.1 - - - +
137D LEU* 1.3 60.3 + - - +
167D ASN* 2.9 28.8 - - + +
169D PHE* 3.6 29.0 - - + -
239D THR* 4.5 2.8 - - - +
242D LEU* 5.6 0.4 - - - +
252D LEU* 5.5 2.2 - - + +
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Residues in contact with LEU 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D HIS* 5.1 0.4 - - - -
7D ILE* 3.1 35.9 - - + +
9D ALA* 4.3 10.3 - - + +
136D GLN* 1.3 75.0 - - - +
138D THR* 1.3 78.7 + - - +
139D HIS* 4.0 26.2 - - + +
150D GLY* 4.6 11.0 - - - +
153D LEU* 5.2 2.2 - - + -
154D ILE* 3.6 31.4 - - + -
166D MET* 5.5 5.2 - - + -
167D ASN 2.8 8.5 + - - +
168D THR* 3.2 21.7 - - + -
169D PHE* 3.0 27.2 + - - +
194D LEU* 5.9 0.2 - - + -
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Residues in contact with THR 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D HIS* 3.7 14.4 + - - +
7D ILE 3.4 1.8 + - - -
8D GLN* 3.3 27.7 - - - +
9D ALA 3.2 22.9 + - - +
13D GLY* 3.7 5.0 + - - -
16D ILE* 3.7 30.2 - - + +
17D GLY* 4.5 2.6 - - - -
137D LEU* 1.3 76.8 - - - +
139D HIS* 1.3 64.4 + - - +
169D PHE* 3.5 30.7 - - + -
235D MET* 4.2 7.6 - - - -
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Residues in contact with HIS 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D ALA 3.7 15.3 - - - +
12D CYS* 4.5 2.5 - - - -
13D GLY* 3.9 6.5 - - - -
16D ILE* 5.6 1.0 - - - +
137D LEU* 4.0 22.4 - - + +
138D THR* 1.3 78.3 - - - +
140D SER* 1.3 68.0 + - - +
141D LEU* 3.4 17.9 - - + +
146D GLY 3.1 27.6 - - - +
147D SER* 4.1 4.3 - - - -
150D GLY* 4.9 2.7 - - - -
151D THR* 5.0 5.1 + - - +
168D THR* 4.1 13.9 - - + -
169D PHE 3.4 6.8 + - - +
170D SER* 2.8 34.7 - - - -
171D VAL* 3.3 24.8 + - - +
194D LEU* 4.3 10.0 - - + +
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Residues in contact with SER 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D ALA 4.9 0.4 + - - -
10D GLY* 5.2 0.9 + - - -
12D CYS* 3.4 11.9 + - - +
13D GLY 4.6 0.8 + - - +
139D HIS* 1.3 75.7 - - - +
141D LEU* 1.3 57.1 + - - +
142D GLY 3.4 1.1 + - - -
146D GLY* 4.9 1.2 - - - -
147D SER* 2.7 35.7 + - - -
171D VAL* 3.4 18.6 - - - -
603D GDP 3.0 57.4 + - - -
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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