Contacts of the strand formed by residues 219 - 224 (chain A) in PDB entry 1ASA
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 219 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A LEU* 3.9 36.1 - - + -
130A THR* 5.4 5.6 - - + -
132A VAL* 5.5 1.6 - - + -
184A GLY* 5.0 5.1 - - - +
185A ASP 2.8 14.2 + - - +
186A VAL* 3.2 15.1 - - + +
187A VAL 3.0 22.8 + - - -
217A GLY 3.8 1.8 + - - -
218A TRP* 1.3 71.0 - - - +
220A PRO* 1.4 66.8 - - - +
221A LEU* 6.2 0.2 - - + -
249A GLU* 3.7 40.4 - - + +
250A LEU* 4.1 7.9 - - - -
251A ILE* 4.5 9.9 - - + -
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Residues in contact with PRO 220 (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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187A VAL* 3.5 7.2 - - + +
189A PHE* 4.6 3.6 - - + -
213A SER* 4.3 3.4 - - - +
218A TRP* 3.4 7.9 - - + +
219A LEU* 1.4 87.8 - - - +
221A LEU* 1.3 62.1 + - - +
222A PHE* 4.1 11.9 - - + -
243A PHE* 3.8 30.1 - - + -
247A HIS* 3.7 26.0 - - + +
249A GLU 3.8 18.8 - - - +
250A LEU* 3.7 9.8 - - + +
251A ILE* 3.2 23.6 + - - +
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Residues in contact with LEU 221 (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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119A LEU* 3.9 24.7 - - + -
122A ALA* 4.4 12.8 - - + -
126A LEU* 4.5 11.2 - - + -
135A VAL* 6.1 0.2 - - + -
149A PHE* 4.3 22.2 - - + -
186A VAL* 3.7 27.1 - - + -
187A VAL 3.1 7.7 + - - +
188A LEU* 3.1 12.0 - - + +
189A PHE 2.8 27.5 + - - +
220A PRO* 1.3 74.4 - - - +
222A PHE* 1.3 75.6 + - - +
251A ILE* 3.2 36.3 - - + +
253A ALA* 4.6 1.1 - - + -
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Residues in contact with PHE 222 (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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189A PHE* 3.5 28.0 - + + -
190A HIS 4.7 0.2 - - - -
191A GLY* 3.8 29.2 - - - -
206A TRP* 4.3 8.5 - - - -
220A PRO* 4.3 10.1 - - + -
221A LEU* 1.3 79.6 - - - +
223A ASP* 1.3 58.4 + - - +
224A PHE* 3.6 5.0 + + + -
239A GLY 4.4 0.7 - - - -
240A LEU* 3.7 44.4 - - + -
243A PHE* 3.8 46.0 - + + -
250A LEU* 5.2 2.7 - - + -
251A ILE 3.0 8.1 + - - -
252A VAL* 4.0 19.2 - - + +
253A ALA* 2.9 29.5 + - - +
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Residues in contact with ASP 223 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A GLY* 5.4 3.1 - - - +
119A LEU* 3.6 14.1 - - + +
145A HIS* 2.7 35.8 + - + +
188A LEU* 4.2 9.3 - - + +
189A PHE 2.8 15.3 + - - +
190A HIS* 3.6 6.6 - - + +
191A GLY 2.9 26.8 + - - -
192A CYS 4.8 1.9 + - - +
221A LEU* 3.7 1.4 + - - +
222A PHE* 1.3 71.1 - - - +
224A PHE* 1.3 56.6 + - - +
225A ALA* 4.0 7.6 + - - +
253A ALA* 3.7 10.8 - - - +
255A SER* 5.9 0.7 - - - -
409A PLP 2.9 40.4 + - + +
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Residues in contact with PHE 224 (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 LEU* 4.3 10.1 - - + -
191A GLY* 3.3 33.2 - - - +
192A CYS* 4.7 6.3 - - - +
222A PHE* 3.6 12.3 + + + -
223A ASP* 1.3 70.0 + - - +
225A ALA* 1.3 54.7 + - - +
226A TYR 3.8 0.2 - - - -
227A GLN* 3.6 52.9 - - + +
236A ASP 3.3 26.5 - - - -
237A ALA* 3.5 13.9 - - + -
240A LEU* 3.8 28.9 - - + -
252A VAL* 4.4 9.6 - - + -
253A ALA 2.9 11.8 + - - +
254A SER* 3.2 9.9 + - - +
255A SER 2.8 31.7 + - - +
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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