Contacts of the strand formed by residues 267 - 275 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263B ARG* 3.4 29.5 - - - +
264B VAL 2.9 16.4 + - - -
265B ALA 2.9 0.4 - - - -
266B GLU* 1.3 79.6 - - - +
268B THR* 1.3 63.8 + - - +
269B GLN* 3.6 14.0 + - - +
286B LEU 4.4 0.3 - - - +
288B LYS* 4.0 27.1 + - - +
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Residues in contact with THR 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262B ARG 3.4 0.5 - - - +
263B ARG* 3.4 3.5 - - - -
264B VAL* 3.0 39.5 + - + +
265B ALA 3.2 15.8 + - - -
266B GLU* 3.8 9.0 + - - +
267B SER* 1.3 76.6 - - - +
269B GLN* 1.3 59.9 + - - +
270B VAL* 5.0 0.4 - - + -
285B ILE* 3.4 32.1 - - + -
286B LEU 3.7 6.7 - - - +
287B PRO* 3.8 13.9 - - + +
291B LYS* 4.8 0.5 - - - +
296B VAL* 4.0 23.3 - - + +
307B GLU* 4.7 8.1 - - - +
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Residues in contact with GLN 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261B TYR* 4.1 24.0 + - + +
262B ARG 3.6 3.4 - - - -
263B ARG* 4.8 7.2 + - + -
267B SER 3.7 11.3 + - - +
268B THR* 1.3 80.1 - - - +
270B VAL* 1.3 61.3 + - - +
271B LEU 3.7 1.0 + - - -
284B LEU 3.0 12.8 - - - +
285B ILE* 3.3 1.7 - - - -
286B LEU* 2.9 53.5 + - - +
287B PRO 4.9 0.8 + - - -
288B LYS* 5.7 1.0 - - - +
401B VAL 4.8 3.1 - - - +
402B THR 4.0 16.0 + - - +
403B PHE* 3.5 33.1 - - + +
404B LYS 5.5 0.6 - - - +
407B ARG* 4.4 5.5 - - - +
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Residues in contact with VAL 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B TYR* 3.1 8.7 - - - -
262B ARG* 2.9 54.7 + - + +
264B VAL* 3.9 5.4 - - + -
268B THR* 5.0 2.2 - - + -
269B GLN* 1.3 70.6 - - - +
271B LEU* 1.3 61.5 + - - +
283B VAL* 4.7 7.0 - - + -
284B LEU 3.4 2.9 - - - +
285B ILE* 3.9 25.4 - - + -
307B GLU* 3.6 37.7 - - + +
308B TRP* 5.3 2.9 - - + +
311B GLU* 3.3 29.6 - - - +
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Residues in contact with LEU 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259B PHE* 3.8 23.3 - - + -
260B ARG 3.9 3.1 - - - +
261B TYR* 4.4 2.9 - - + +
269B GLN 3.7 1.0 + - - -
270B VAL* 1.3 74.5 - - - +
272B GLU* 1.3 63.3 + - - +
273B LEU* 3.9 25.1 - - + -
283B VAL* 3.2 5.8 - - - +
284B LEU* 2.8 38.5 + - + +
317B LEU* 3.8 28.7 - - + -
319B VAL* 3.8 18.6 - - + -
403B PHE* 3.6 46.4 - - + -
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Residues in contact with GLU 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259B PHE* 3.5 18.0 - - - +
260B ARG* 2.9 55.1 + - + +
270B VAL 4.1 0.2 + - - -
271B LEU* 1.3 73.5 - - - +
273B LEU* 1.3 58.6 + - - +
274B PRO* 3.4 9.0 - - - +
281B THR* 2.9 32.6 + - + +
283B VAL* 3.7 4.7 - - + -
308B TRP* 3.2 38.1 - - - -
311B GLU* 3.1 26.4 - - - +
416B VAL* 4.5 1.0 - - - +
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Residues in contact with LEU 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B TRP* 4.0 25.6 - - + -
228B SER 6.1 0.7 - - - +
230B PHE* 4.5 15.7 - - + -
255B GLN* 5.0 0.9 - - - +
259B PHE* 3.5 36.3 - - + -
271B LEU* 3.9 29.6 - - + -
272B GLU* 1.3 70.4 - - - +
274B PRO* 1.3 65.1 - - + +
275B PHE* 3.6 3.6 + - - -
281B THR* 4.2 0.9 - - - -
282B MET* 2.9 39.9 + - - +
284B LEU* 4.3 10.5 - - + -
319B VAL* 5.2 1.6 - - + -
321B MET* 4.0 26.0 - - - -
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Residues in contact with PRO 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B TRP* 4.1 4.6 - - - +
227B LYS* 3.1 37.1 + - + +
228B SER* 4.6 3.2 + - - +
259B PHE* 4.8 11.9 - - + -
260B ARG* 3.2 31.4 - - - +
272B GLU 3.4 9.6 - - - +
273B LEU* 1.3 84.3 - - - +
275B PHE* 1.3 66.9 + - - +
278B ASP* 4.4 15.3 - - - +
280B ILE 4.2 1.6 - - - +
281B THR* 3.7 9.6 - - - +
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Residues in contact with PHE 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B SER 5.0 1.3 - - - +
139B SER* 5.3 1.1 - - - -
222B PHE* 4.0 22.7 - + + -
224B GLY* 3.1 37.2 - - - -
225B LEU 3.5 6.1 - - - +
226B TRP* 3.4 19.3 - + - -
227B LYS* 4.0 7.3 - - - +
273B LEU 3.9 0.9 - - - -
274B PRO* 1.3 78.6 - - - +
276B LYS* 1.3 71.6 + - + +
277B GLY 3.4 0.3 + - - -
278B ASP* 3.1 17.2 + - - +
280B ILE* 3.2 34.3 + - + +
281B THR 3.6 5.6 - - - -
282B MET* 3.5 29.6 - - + -
381B SER* 3.3 38.8 - - - -
413B ILE* 4.3 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