Contacts of the strand formed by residues 229 - 233 (chain A) in PDB entry 3I7L
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 229 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A LEU* 4.6 5.8 - - + -
179A CYS* 3.8 29.6 - - + -
207A TRP* 4.9 3.4 - - + -
219A VAL* 4.5 6.7 - - + -
220A ILE 3.2 9.2 - - - +
221A ALA* 5.1 1.1 - - + -
228A GLY* 1.3 75.0 - - - +
230A ILE* 1.3 67.8 + - - +
231A ILE* 3.9 6.4 + - + +
238A THR 3.5 2.3 - - - +
239A TYR* 3.9 2.2 - - - -
240A HIS* 3.0 38.4 + - + +
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Residues in contact with ILE 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A VAL* 3.4 3.5 - - - +
220A ILE* 2.8 40.4 + - + +
222A VAL* 3.7 20.0 - - + -
229A ALA* 1.3 76.6 - - - +
231A ILE* 1.3 69.3 - - - +
232A ILE* 4.1 17.5 - - + -
237A ILE* 4.0 23.6 - - + -
238A THR 3.4 7.0 - - - +
239A TYR* 3.8 19.3 - - + -
271A TYR* 4.3 12.6 - - + -
283A LEU* 4.4 11.2 - - + -
285A LEU* 3.8 33.0 - - + -
300A LEU* 5.5 3.1 - - + -
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Residues in contact with ILE 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A CYS* 5.7 0.4 - - - -
181A VAL* 4.2 12.3 - - + -
190A VAL* 3.6 26.2 - - + -
212A VAL* 4.2 12.6 - - + -
213A GLU* 5.6 0.4 - - + +
216A ALA* 3.6 29.2 - - + -
218A MET 3.4 7.2 - - - +
219A VAL* 4.5 5.8 - - + -
229A ALA* 4.2 11.9 - - + +
230A ILE* 1.3 80.0 - - - +
232A ILE* 1.3 62.7 + - - +
233A GLY 3.8 0.7 + - - -
236A SER 3.9 0.7 - - - +
237A ILE* 3.6 5.0 - - - -
238A THR* 2.9 37.7 + - + +
240A HIS* 3.2 33.4 - - + +
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Residues in contact with ILE 232 (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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216A ALA* 3.5 2.1 - - - -
217A SER* 2.6 33.5 + - - +
218A MET* 3.0 35.8 + - + +
220A ILE* 3.7 32.1 - - + -
230A ILE* 4.1 13.9 - - + -
231A ILE* 1.3 72.4 - - - +
233A GLY* 1.3 59.4 + - - +
236A SER 4.1 3.8 - - - +
237A ILE* 4.4 18.2 - - + -
258A ILE* 3.7 42.8 - - + +
261A HIS* 5.2 2.9 - - + -
273A LEU* 4.8 9.9 - - + -
283A LEU* 5.1 4.3 - - + -
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Residues in contact with GLY 233 (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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213A GLU* 3.1 14.6 - - - -
215A GLU 3.5 13.2 - - - -
216A ALA* 3.6 3.4 - - - -
217A SER* 5.0 1.3 - - - -
231A ILE 3.8 0.8 + - - -
232A ILE* 1.3 82.4 - - - +
234A GLN* 1.3 69.5 + - - -
235A GLU 3.4 1.0 + - - -
236A SER 2.9 18.6 + - - +
253A ILE* 4.3 5.5 - - - +
258A ILE* 5.6 3.6 - - - +
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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