Contacts of the strand formed by residues 230 - 237 (chain A) in PDB entry 2D2I
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 230 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A LEU* 4.9 10.5 - - + -
164A ALA* 4.7 9.0 - - + -
173A ILE* 4.5 7.9 - - + -
176A GLY* 3.4 31.0 - - - +
177A THR 5.6 0.2 - - - -
178A MET* 6.2 0.9 - - + -
216A ALA* 3.7 22.8 - - + +
217A LYS* 4.2 8.8 + - - +
219A VAL* 3.7 38.6 - - + -
226A LEU* 4.1 16.9 + - + +
228A GLY* 3.6 4.2 - - - +
229A LYS* 1.3 87.5 + - + +
231A ASN* 1.3 68.8 + - - +
247A LEU* 4.3 8.5 - - + -
249A VAL* 4.1 15.3 - - + -
305B MET* 4.8 2.6 - - - +
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Residues in contact with ASN 231 (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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176A GLY 3.4 4.2 + - - -
177A THR* 3.3 19.3 + - - -
178A MET* 2.8 23.9 + - - +
216A ALA* 3.2 19.5 - - - +
217A LYS* 4.8 10.1 - - + +
230A LEU* 1.3 81.1 - - - +
232A GLY* 1.3 61.4 + - - +
303B LEU* 2.7 37.1 - - + +
305B MET* 3.6 23.1 - - + +
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Residues in contact with GLY 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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177A THR* 4.3 1.6 - - - -
178A MET* 2.8 14.4 - - - -
212A THR* 5.6 0.5 - - - -
213A THR* 3.6 21.6 + - - +
216A ALA* 3.9 3.9 - - - +
231A ASN* 1.3 86.0 - - - +
233A ILE* 1.3 71.2 + - - +
303B LEU* 4.0 9.4 - - - +
311B LYS* 5.0 0.9 - - - -
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Residues in contact with ILE 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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178A MET* 2.9 3.1 + - - +
179A THR* 3.2 25.2 - - + +
180A THR* 3.1 23.7 + - - +
210A PRO* 5.8 0.2 - - + -
211A THR 4.3 5.6 - - - +
212A THR* 5.3 1.6 - - - +
213A THR* 3.6 12.2 - - - +
232A GLY* 1.3 81.5 - - - +
234A ALA* 1.3 68.1 + - - +
235A LEU* 4.6 10.5 - - + -
301B LEU* 4.6 30.3 - - + +
303B LEU* 4.2 14.4 - - + -
311B LYS* 4.1 5.8 - - - -
313B ILE* 3.8 35.7 - - + -
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Residues in contact with ALA 234 (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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180A THR* 3.3 25.4 - - + +
182A HIS* 5.3 0.9 - - + -
200A ARG* 6.0 0.2 - - - +
210A PRO* 3.4 5.4 - - - +
211A THR* 3.0 50.4 + - + +
212A THR 4.5 0.2 - - - +
213A THR* 4.1 11.2 - - - -
233A ILE* 1.3 77.4 - - - +
235A LEU* 1.3 67.3 + - - +
236A ARG* 4.1 6.7 - - - +
1339A SO4 5.4 1.8 - - - +
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Residues in contact with LEU 235 (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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179A THR* 4.1 20.9 - - + -
180A THR 2.8 11.7 + - - +
181A THR* 3.3 9.3 - - - +
182A HIS 2.8 24.5 + - - -
208A ILE* 4.4 16.8 - - + -
209A VAL 3.5 3.4 - - - -
210A PRO* 4.1 24.2 - - + -
233A ILE* 4.6 11.0 - - + -
234A ALA* 1.3 80.1 - - - +
236A ARG* 1.3 65.6 + - - +
237A VAL* 3.6 4.0 + - + +
181B THR* 3.6 31.4 - - + +
244B VAL* 4.2 14.1 - - + -
246B ASP* 5.8 6.1 - - + +
313B ILE* 5.3 9.9 - - + -
315B TRP* 5.3 1.1 - - + -
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Residues in contact with ARG 236 (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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182A HIS* 3.1 38.9 + - - +
183A SER 3.2 5.9 + - - -
184A TYR* 4.8 1.6 - - - -
185A THR* 3.2 24.9 + - - +
188A GLN* 2.7 60.4 + - + +
200A ARG* 3.5 24.9 - - - +
204A ALA 5.7 0.2 - - - -
207A ASN 3.6 2.1 - - - +
208A ILE* 3.3 4.5 - - - -
209A VAL* 2.7 45.3 + - + +
211A THR* 3.9 20.5 - - + +
234A ALA* 5.1 3.3 - - - +
235A LEU* 1.3 73.1 - - - +
237A VAL* 1.3 60.2 + - - +
1340A SO4 3.1 34.1 + - - -
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Residues in contact with VAL 237 (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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181A THR* 3.8 22.9 - - + -
182A HIS 2.9 11.5 + - - +
184A TYR* 3.5 14.6 + - - -
204A ALA 4.4 1.3 - - - -
207A ASN 4.1 1.6 - - - -
208A ILE* 4.2 21.3 - - + -
235A LEU* 3.9 3.6 - - + +
236A ARG* 1.3 79.0 - - - +
238A PRO* 1.3 62.5 - - + +
239A THR* 2.7 29.6 + - + +
181B THR* 4.2 10.8 - - + -
208B ILE* 3.8 32.8 - - + -
237B VAL* 4.3 8.3 - - + -
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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