Contacts of the strand formed by residues 237 - 242 (chain A) in PDB entry 1IS2
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 ASN 237 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176A TRP* 2.8 34.1 + - + +
177A PRO 3.6 2.5 - - - -
178A GLY* 3.9 5.0 - - - -
225A ASP* 3.2 8.5 + - - +
226A ILE* 2.9 44.4 + - + +
229A LYS* 2.7 27.7 + - - +
232A TYR* 3.7 8.0 - - - -
235A MET* 3.1 28.1 + - - +
236A ASP* 1.3 70.1 - - - +
238A GLY* 1.3 58.3 + - - +
699A FAD 3.7 22.4 + - - -
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Residues in contact with GLY 238 (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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175A TRP* 3.5 0.2 - - - -
176A TRP 2.8 29.4 + - - -
177A PRO* 2.9 22.1 + - - +
180A LEU* 3.8 6.1 - - - -
181A GLY 3.7 13.0 - - - -
224A GLY 3.2 11.4 - - - -
226A ILE* 3.4 8.1 - - - -
236A ASP 3.2 1.4 + - - -
237A ASN* 1.3 75.0 - - - +
239A TYR* 1.3 58.2 + - - -
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Residues in contact with TYR 239 (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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173A ILE* 3.9 4.5 - - + -
174A LYS 2.9 14.6 - - - +
175A TRP* 3.4 35.9 - + + -
180A LEU* 3.8 4.6 - - - +
222A THR* 4.0 18.9 - - + +
223A VAL* 3.3 26.9 + - - +
224A GLY* 2.9 41.1 + - - -
225A ASP 3.3 24.2 - - - -
226A ILE* 4.3 1.1 - - + -
238A GLY* 1.3 74.9 - - - -
240A LEU* 1.3 63.4 + - - +
241A LYS 4.9 0.2 - - - -
633B PHE* 3.8 27.4 - + - -
636B ALA* 4.3 9.9 - - + -
637B LYS* 4.3 13.1 - - - +
642B ASN* 4.2 11.1 + - - -
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Residues in contact with LEU 240 (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 ALA* 4.9 0.7 - - + -
167A SER* 4.0 4.0 + - - -
173A ILE* 3.3 5.5 - - - +
174A LYS* 2.9 39.8 + - + +
180A LEU* 3.7 23.1 - - + -
187A ALA* 4.5 4.0 - - + -
189A VAL* 4.0 15.3 - - + -
209A ILE* 4.0 21.3 - - + -
221A ILE* 3.8 13.7 - - + -
222A THR 3.4 2.9 - - - +
223A VAL* 3.1 27.1 - - + -
239A TYR* 1.3 75.5 - - - +
241A LYS* 1.3 66.1 + - - +
242A MET* 4.0 32.4 - - + +
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Residues in contact with LYS 241 (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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167A SER* 3.6 25.8 - - - +
169A THR 6.0 1.3 - - - -
173A ILE* 4.0 27.8 - - + +
220A GLY 3.6 3.3 - - - +
221A ILE* 3.8 1.9 - - - -
222A THR* 2.9 56.2 + - + +
239A TYR* 5.7 0.7 - - + -
240A LEU* 1.3 74.9 - - - +
242A MET* 1.3 67.9 + - - +
243A ASP* 5.5 13.4 - - + +
633B PHE* 5.7 2.7 - - + -
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Residues in contact with MET 242 (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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152A THR* 3.9 14.4 - - + -
165A LEU* 3.7 34.8 - - - +
166A ASN* 3.4 1.6 - - - +
167A SER* 2.8 52.4 + - - +
174A LYS* 4.4 10.1 - - + -
189A VAL* 3.9 31.4 - - + -
207A VAL* 4.6 9.2 - - - -
220A GLY 3.7 3.4 - - - -
221A ILE* 4.0 17.0 - - + -
240A LEU* 4.0 28.5 - - + +
241A LYS* 1.3 79.7 - - - +
243A ASP* 1.3 59.9 + - - +
244A ASN 3.3 4.7 + - - -
245A TYR* 4.1 7.4 - - + -
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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