Contacts of the strand formed by residues 266 - 273 (chain A) in PDB entry 3A4T
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 PHE 266 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A SER* 3.7 23.6 - - - -
72A SER* 4.0 15.3 - - - -
75A PRO* 4.0 18.4 - - + -
97A LYS* 3.9 22.0 - - - -
163A ASP* 3.8 17.0 - - - -
210A SER* 4.4 1.6 - - - -
211A THR 3.3 21.5 - - - -
212A CYS* 3.9 15.3 - - + -
213A SER 3.8 5.0 - - - +
214A MET* 4.2 2.7 - - - +
258A ARG* 3.4 7.4 - - - +
259A VAL* 2.8 47.0 + - + +
264A GLU* 3.1 30.1 - - - +
265A PRO* 1.3 83.4 - - - +
267A PHE* 1.3 70.2 + - - +
268A ILE* 4.4 4.5 - - + -
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Residues in contact with PHE 267 (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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209A TYR* 4.0 17.7 - + - -
210A SER* 3.1 27.2 - - - -
211A THR* 3.1 13.1 + - + +
213A SER 3.6 0.4 - - - +
219A ASN* 3.2 68.9 - - + +
220A GLU* 3.8 20.4 - - + -
223A ILE* 3.8 19.1 - - + -
251A GLY* 4.7 0.4 - - - -
256A THR* 3.3 38.1 - - + -
257A LEU 3.1 24.0 - - - -
258A ARG* 4.3 7.9 - - + -
266A PHE* 1.3 75.7 - - - +
268A ILE* 1.3 61.9 + - - +
269A ALA* 4.2 6.5 - - + -
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Residues in contact with ILE 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A SER 4.9 0.2 - - - +
74A ILE* 3.8 26.5 - - + -
75A PRO* 4.1 18.4 - - + -
78A VAL* 4.1 17.9 - - + -
208A VAL* 3.6 25.6 - - + -
209A TYR 3.4 3.4 - - - +
238A ILE* 3.6 21.9 - - + +
248A ILE* 4.4 7.4 - - + -
256A THR* 3.7 1.2 - - - -
257A LEU* 2.9 43.1 + - + +
259A VAL* 3.9 27.6 - - + -
266A PHE* 4.4 7.6 - - + -
267A PHE* 1.3 83.3 - - - +
269A ALA* 1.3 65.1 + - - +
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Residues in contact with ALA 269 (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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208A VAL* 3.2 9.1 - - - +
209A TYR* 2.8 35.7 + - - +
223A ILE* 3.8 32.5 - - + -
235A LEU* 4.8 2.9 - - + -
238A ILE* 3.8 7.9 - - - -
256A THR* 3.8 25.4 - - + +
267A PHE* 4.2 3.5 - - + -
268A ILE* 1.3 77.0 - - - +
270A LYS* 1.4 60.2 + - - +
271A LEU* 5.6 0.7 - - - -
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Residues in contact with LYS 270 (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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78A VAL* 2.7 41.9 + - + +
79A LEU* 3.5 11.9 + - - +
80A ASN* 4.9 2.2 - - - +
159A LYS* 4.5 0.8 - - - +
206A GLU* 2.8 44.5 + - - -
207A LEU 3.2 10.1 - - - +
208A VAL* 3.9 8.1 - - + -
235A LEU* 3.7 6.5 - - - +
236A ILE* 2.7 59.2 + - + +
238A ILE* 4.2 12.2 - - + +
255A GLY 5.4 0.4 + - - -
269A ALA* 1.4 77.7 - - - +
271A LEU* 1.3 61.1 + - - +
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Residues in contact with LEU 271 (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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194A ILE* 3.9 26.7 - - + -
198A ILE* 3.9 21.8 - - + -
201A LEU* 5.3 1.1 - - + -
206A GLU* 3.3 8.5 - - - +
207A LEU* 2.8 47.7 + - + +
209A TYR* 5.4 0.9 - - + -
223A ILE* 4.6 9.9 - - + -
226A ILE* 4.2 8.7 - - + -
227A LEU* 4.2 15.7 - - + -
233A VAL* 3.8 19.3 - - + -
234A GLU 3.2 7.9 - - - +
235A LEU* 3.8 27.6 - - + -
236A ILE* 3.9 4.4 - - - +
270A LYS* 1.3 75.4 - - - +
272A ARG* 1.3 61.4 + - - +
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Residues in contact with ARG 272 (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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201A LEU* 4.8 1.3 - - - -
204A ASP* 4.2 24.6 + - - +
205A GLY 3.3 10.5 - - - +
206A GLU* 4.8 2.9 - - + +
233A VAL* 3.3 6.2 - - - -
234A GLU* 2.7 63.1 + - + +
236A ILE* 3.8 28.1 - - + +
271A LEU* 1.3 75.3 - - - +
273A LYS* 1.3 84.4 + - - +
274A ILE* 3.5 17.2 + - - +
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Residues in contact with LYS 273 (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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156A PHE* 5.4 1.8 - - - -
198A ILE* 2.8 35.2 + - + -
199A ASP* 3.3 13.5 + - - +
201A LEU* 2.8 38.3 + - + +
202A LYS 3.7 19.5 - - - +
203A LYS* 4.5 5.4 - - + +
204A ASP* 2.8 30.3 + - - +
205A GLY 3.0 9.3 + - - -
230A ARG* 4.0 3.5 - - - +
232A ASP* 3.2 35.9 - - + +
233A VAL* 4.6 1.6 - - - +
272A ARG* 1.3 74.9 - - - +
274A ILE* 1.3 65.8 + - - +
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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