Contacts of the strand formed by residues 267 - 275 (chain A) in PDB entry 1ATT
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 SER 267 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263A ARG* 4.7 23.4 + - - +
264A VAL 2.9 16.3 + - - -
266A GLU* 1.3 69.4 - - - +
268A THR* 1.3 59.2 + - - +
269A GLN* 3.7 8.6 + - - +
286A LEU 4.4 0.2 - - - +
288A LYS* 2.9 56.8 + - - +
291A LYS* 4.3 0.4 + - - -
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Residues in contact with THR 268 (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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264A VAL* 2.9 29.2 + - + +
265A ALA 3.2 18.0 + - - +
266A GLU* 2.9 12.5 + - - +
267A SER* 1.3 73.6 - - - +
269A GLN* 1.3 60.2 + - - +
270A VAL* 4.7 4.7 - - + -
285A ILE* 4.1 24.9 - - + -
287A PRO* 3.6 22.3 - - + +
291A LYS* 4.3 2.6 - - - +
296A VAL* 4.4 14.0 - - + +
307A GLU* 4.3 17.7 - - - +
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Residues in contact with GLN 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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261A TYR* 2.7 38.9 + - + +
262A ARG 3.8 6.3 - - - -
263A ARG* 3.7 27.4 - - + +
267A SER 3.7 4.9 - - - +
268A THR* 1.3 73.1 - - - +
270A VAL* 1.3 58.2 + - - +
271A LEU 4.1 0.4 - - - -
284A LEU 3.4 1.0 - - - +
285A ILE* 3.4 3.8 - - - -
286A LEU* 2.9 63.8 + - - +
288A LYS* 6.5 0.2 - - - -
402A THR 3.1 23.4 + - - -
403A PHE* 3.8 19.1 - - + +
404A LYS 4.8 0.7 + - - -
407A ARG* 5.0 0.9 + - - -
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Residues in contact with VAL 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A TYR* 3.4 25.6 - - - -
262A ARG 3.4 10.1 + - - +
264A VAL* 3.6 24.7 - - + -
268A THR* 4.0 7.2 - - + +
269A GLN* 1.3 75.8 - - - +
271A LEU* 1.3 58.2 + - - +
283A VAL* 3.4 32.5 - - + -
284A LEU 3.2 4.0 - - - +
285A ILE* 4.1 13.7 - - + -
307A GLU* 3.8 20.9 - - + +
308A TRP* 5.1 2.5 - - + +
311A GLU* 3.5 25.9 - - - +
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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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259A PHE* 4.0 17.0 - - + -
260A ARG 3.9 5.6 - - - +
261A TYR* 4.5 2.0 - - + -
269A GLN 4.1 0.8 - - - -
270A VAL* 1.3 74.8 - - - +
272A GLU* 1.3 81.3 + - - +
273A LEU* 3.3 39.9 - - + -
282A MET 3.8 0.2 - - - +
283A VAL* 3.3 6.4 - - - +
284A LEU* 3.0 33.8 + - + +
311A GLU* 5.0 0.4 - - - -
317A LEU* 4.8 7.6 - - + -
319A VAL* 3.9 23.1 - - + -
403A PHE* 3.5 48.0 - - + -
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Residues in contact with GLU 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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259A PHE* 4.0 10.0 - - - +
260A ARG* 2.7 62.8 + - + +
271A LEU* 1.3 83.1 - - - +
273A LEU* 1.3 56.9 + - - +
274A PRO* 3.7 8.0 - - - +
281A THR* 3.3 38.6 + - + +
282A MET 3.4 4.3 - - - +
283A VAL* 3.9 11.8 - - + +
308A TRP* 5.0 2.6 - - - +
311A GLU* 3.8 20.9 + - - +
312A LEU* 5.2 0.9 - - - +
414A ARG* 4.2 9.5 - - - -
416A VAL* 4.6 4.8 - - - +
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Residues in contact with LEU 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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226A TRP* 3.8 28.3 - - + -
230A PHE* 4.0 13.7 - - + -
259A PHE* 3.7 34.5 - - + -
271A LEU* 3.3 21.5 - - + -
272A GLU* 1.3 70.3 - - - +
274A PRO* 1.3 67.1 - - + +
275A PHE* 3.8 0.5 + - - -
281A THR* 4.0 0.8 - - - -
282A MET* 2.9 31.2 + - + +
284A LEU* 4.1 19.5 - - + -
319A VAL* 4.7 1.3 - - + -
321A MET* 3.5 35.4 - - + -
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Residues in contact with PRO 274 (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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226A TRP* 4.1 5.5 - - - +
227A LYS* 3.2 30.4 + - + +
228A SER* 4.8 1.0 + - - +
259A PHE* 4.4 16.2 - - + -
260A ARG* 3.2 28.3 - - - +
272A GLU 3.7 6.5 - - - +
273A LEU* 1.3 87.5 - - - +
275A PHE* 1.3 67.9 + - - +
278A ASP* 3.8 19.5 - - - +
280A ILE 3.9 1.8 - - - +
281A THR* 3.9 20.6 - - + -
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Residues in contact with PHE 275 (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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138A SER 4.9 4.7 - - - +
139A SER* 5.1 1.8 - - - +
222A PHE* 3.5 23.1 - + + -
224A GLY* 3.7 22.4 - - - -
225A LEU 3.3 17.3 - - - +
226A TRP* 3.9 24.2 - + - -
227A LYS* 4.0 7.5 - - - +
273A LEU 4.3 0.7 - - - -
274A PRO* 1.3 80.3 - - - +
276A LYS* 1.3 61.1 + - - +
277A GLY 2.9 10.4 + - - -
278A ASP* 3.4 11.1 + - - -
279A ASP 5.8 0.2 - - - -
280A ILE* 3.2 36.3 + - + +
281A THR 3.2 28.7 - - - -
282A MET* 3.5 13.0 - - + -
381A SER* 3.1 28.5 - - - -
413A ILE* 4.8 1.8 - - + -
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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