Contacts of the strand formed by residues 223 - 230 (chain T) in PDB entry 3P71
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 223 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84T PHE* 4.8 1.6 - - - -
193T THR 3.2 13.2 - - - +
195T LEU* 4.7 0.9 - - + -
216T ALA 4.8 1.3 - - - +
220T PHE* 3.7 28.5 - - + +
221T GLU 4.2 0.2 - - - -
222T ARG* 1.3 76.1 - - - +
224T MET* 1.3 62.7 + - - +
273T TRP* 3.6 22.0 - - + -
321T THR* 3.5 4.7 - - - -
322T LYS* 3.1 33.5 + - + +
329T LEU* 4.3 8.2 - - - +
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Residues in contact with MET 224 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80T LEU* 4.1 16.4 - - + +
84T PHE* 3.8 37.2 - - + -
193T THR 2.8 8.1 + - - +
194T LEU* 3.4 10.7 - - + -
195T LEU* 2.8 35.4 + - - +
223T ALA* 1.3 75.2 - - - +
225T PHE* 1.3 60.5 + - - +
226T ILE* 3.8 18.2 - - + -
273T TRP* 3.7 3.8 - - - -
319T TRP* 3.8 35.9 - - + -
320T ALA 3.4 13.5 - - - +
321T THR* 4.0 10.1 - - + -
329T LEU* 5.2 0.7 - - + -
332T ILE* 4.1 23.1 - - + -
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Residues in contact with PHE 225 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97T LEU* 4.0 16.8 - - + -
195T LEU* 3.4 25.1 - - + -
197T ALA* 3.7 24.9 - - + -
201T LEU* 4.3 10.1 - - + -
212T LEU* 5.4 3.8 - - + -
213T LEU* 3.7 36.1 - - + -
216T ALA* 4.4 10.8 - - + -
224T MET* 1.3 73.8 - - - +
226T ILE* 1.3 81.3 + - - +
227T ASN* 4.0 12.7 + - + -
268T LEU* 4.7 3.8 - - + +
273T TRP* 3.7 27.6 - + + -
319T TRP* 3.1 7.3 - - - +
320T ALA* 2.9 39.5 + - + +
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Residues in contact with ILE 226 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77T VAL* 4.2 20.2 - - + -
80T LEU* 3.5 33.4 - - + -
81T ILE* 4.2 20.0 - - + +
194T LEU* 3.6 21.1 - - + -
195T LEU 2.9 10.7 + - - +
196T ILE* 4.3 9.0 - - + -
197T ALA 2.8 29.2 + - - +
198T GLU* 6.2 0.4 - - - -
224T MET* 3.8 19.3 - - + -
225T PHE* 1.3 76.3 - - - +
227T ASN* 1.3 63.8 + - - +
228T TYR* 4.7 1.3 - - + +
317T LEU* 4.2 20.6 - - + -
318T CYS 3.5 8.1 - - - +
319T TRP* 4.4 0.2 - - + -
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Residues in contact with ASN 227 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197T ALA 3.5 9.1 - - - +
201T LEU* 3.3 23.7 + - + +
225T PHE* 4.0 15.4 + - + -
226T ILE* 1.3 73.9 - - - +
228T TYR* 1.3 62.3 + - - +
229T GLU* 3.5 24.6 + - - +
264T GLN* 3.9 9.1 + - - -
267T ARG* 3.4 21.6 - - - +
268T LEU* 5.0 10.5 - - + +
317T LEU* 3.8 0.6 - - - -
318T CYS* 2.8 57.4 + - + +
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Residues in contact with TYR 228 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308C PHE* 3.6 17.8 - - - +
69T GLY 4.7 1.4 + - - -
73T ARG* 3.4 61.1 - - + +
77T VAL* 4.6 2.2 - - + -
197T ALA 3.1 8.3 + - - +
198T GLU* 4.2 15.0 - - + -
199T CYS* 2.7 42.7 + - + -
200T VAL 4.5 0.2 + - - -
226T ILE* 4.1 1.6 - - + +
227T ASN* 1.3 73.0 - - - +
229T GLU* 1.3 65.3 + - - +
281T MET* 3.6 33.9 - - + +
315T TYR* 3.6 31.2 - + + +
316T CYS 3.4 16.2 - - - -
317T LEU* 3.9 18.8 - - + -
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Residues in contact with GLU 229 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199T CYS* 4.7 8.1 - - - +
201T LEU* 3.3 11.3 + - - +
202T VAL* 3.1 29.5 + - + -
227T ASN* 3.5 17.3 + - - +
228T TYR* 1.3 80.7 - - - +
230T GLN* 1.3 69.3 + - - +
257T THR* 4.2 2.1 + - - -
258T CYS* 3.5 17.0 - - - -
264T GLN* 3.0 20.4 + - - +
267T ARG* 2.7 28.2 + - - -
315T TYR* 3.2 11.1 - - - +
316T CYS* 2.8 39.5 + - - +
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Residues in contact with GLN 230 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308C PHE 4.0 5.3 + - - -
309C LEU* 4.8 2.8 - - - +
199T CYS* 4.4 8.2 - - - -
202T VAL* 3.3 36.4 - - + +
203T TYR* 5.3 0.4 + - - -
229T GLU* 1.3 82.4 - - - +
231T VAL* 1.3 59.5 + - - +
233T MET* 3.7 27.4 - - + -
241T MET* 3.0 36.5 - - + +
252T LEU* 4.6 8.8 - - - +
258T CYS* 3.3 15.0 - - - -
264T GLN* 3.2 23.6 + - - -
314T HIS 3.2 8.3 - - - +
315T TYR* 3.5 22.2 + - + +
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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