Contacts of the strand formed by residues 379 - 393 (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 GLU 379 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225A LEU* 3.2 21.6 - - + +
226A TRP* 3.0 22.3 + - - -
229A LYS* 3.5 30.2 - - + +
230A PHE 4.9 0.5 - - - +
232A PRO* 4.5 10.4 - - - +
377A ASN* 2.9 23.1 + - - +
378A GLU* 1.3 88.1 - - - +
380A GLY* 1.3 56.8 + - - +
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Residues in contact with GLY 380 (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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224A GLY 3.0 12.8 - - - -
225A LEU* 4.0 1.3 - - - -
226A TRP* 3.2 26.5 - - - -
377A ASN* 2.9 35.8 + - - +
379A GLU* 1.3 79.1 - - - +
381A SER* 1.3 59.5 + - - -
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Residues in contact with SER 381 (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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222A PHE* 3.3 10.2 - - - -
223A LYS* 4.4 1.6 - - - -
224A GLY 2.9 30.5 + - - -
226A TRP* 4.5 1.4 - - - -
275A PHE* 3.1 28.1 - - - -
282A MET* 3.7 7.5 - - - +
374A LEU* 4.5 5.8 - - - -
375A GLU 3.0 15.7 - - - -
376A VAL* 3.5 20.4 - - - -
377A ASN* 4.8 1.1 - - - +
380A GLY* 1.3 72.6 - - - -
382A GLU* 1.3 61.1 + - - +
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Residues in contact with GLU 382 (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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196A GLU* 4.5 3.5 - - - +
198A ARG* 2.8 47.6 + - + +
221A TYR* 2.9 38.6 + - + +
222A PHE* 3.2 10.5 - - - +
223A LYS* 4.0 24.3 + - + +
373A PHE* 3.8 7.3 - - + -
374A LEU* 3.4 3.5 - - - +
375A GLU* 2.9 34.7 + - + +
381A SER* 1.3 76.1 - - - +
383A ALA* 1.3 57.9 + - - +
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Residues in contact with ALA 383 (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 PHE* 4.3 0.2 - - + -
221A TYR* 3.7 3.8 - - - -
222A PHE* 2.8 39.9 + - + +
373A PHE* 3.3 11.7 - - - +
374A LEU* 4.3 13.2 - - + +
382A GLU* 1.3 73.6 - - - +
384A ALA* 1.3 64.2 + - - +
413A ILE* 4.4 2.7 - - + -
423A PHE* 3.5 37.2 - - + -
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Residues in contact with ALA 384 (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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195A THR* 4.1 8.7 - - - -
198A ARG* 3.9 24.7 - - + -
199A ILE* 3.6 22.4 - - + -
220A ILE 3.3 11.7 - - - +
221A TYR* 4.2 4.3 - - + +
372A ALA* 3.6 0.9 - - - -
373A PHE* 3.1 26.4 + - + -
383A ALA* 1.3 77.0 - - - +
385A ALA* 1.3 60.1 + - - +
423A PHE* 3.1 11.8 - - - -
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Residues in contact with ALA 385 (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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80A SER* 3.3 35.0 - - - +
83A SER* 4.4 6.7 - - - -
195A THR* 3.8 5.0 - - - +
199A ILE* 3.6 5.0 - - - +
219A THR* 3.5 2.8 - - - -
220A ILE* 2.7 32.1 + - + +
370A HIS* 4.5 4.5 - - + +
371A LYS 3.5 11.7 - - - +
372A ALA* 4.8 1.1 - - - -
384A ALA* 1.3 78.4 - - - +
386A SER* 1.3 63.0 + - - +
423A PHE* 3.5 4.7 - - + -
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Residues in contact with SER 386 (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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83A SER* 3.8 4.0 - - - -
191A ILE* 3.0 26.0 - - - +
199A ILE* 3.6 24.2 - - - -
202A VAL* 4.0 10.4 - - - +
217A VAL* 4.1 2.4 - - - +
218A ASN 3.2 12.7 + - - -
370A HIS* 3.0 31.0 + - - -
371A LYS 3.0 8.7 + - - -
385A ALA* 1.3 76.2 - - - +
387A THR* 1.3 67.2 + - - +
388A VAL* 4.5 0.7 - - - +
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Residues in contact with THR 387 (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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83A SER* 3.2 14.6 + - - +
84A ILE* 3.5 9.8 - - + +
87A ALA* 3.5 28.7 - - + +
88A PHE* 4.4 13.5 - - + -
216A LEU 4.2 0.2 - - - +
217A VAL* 3.5 1.7 - - - +
218A ASN* 3.1 28.6 + - - +
332A VAL* 5.6 2.7 - - + -
369A PHE 3.0 12.3 - - - +
370A HIS* 2.8 26.9 + - + -
386A SER* 1.3 69.7 + - - +
388A VAL* 1.3 76.5 + - - +
389A ILE* 4.0 5.4 - - + -
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Residues in contact with VAL 388 (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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191A ILE* 4.9 1.3 - - + -
202A VAL* 4.0 22.2 - - + -
203A ILE* 3.6 41.7 - - + -
208A ILE* 5.7 0.2 - - + -
215A VAL* 3.9 13.0 - - + -
216A LEU 3.4 6.3 - - - +
217A VAL* 4.0 19.5 - - + -
368A ALA* 3.4 1.0 - - - -
369A PHE* 2.7 42.8 + - + +
386A SER* 4.5 4.9 - - - +
387A THR* 1.3 78.3 - - - +
389A ILE* 1.3 65.9 + - - +
390A SER* 4.3 5.4 - - - +
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Residues in contact with ILE 389 (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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87A ALA* 3.8 27.1 - - + +
88A PHE* 4.3 16.6 - - + -
91A THR* 3.2 23.8 - - - +
215A VAL* 4.0 0.3 - - - -
216A LEU* 3.1 49.2 + - + +
365A VAL* 3.8 22.7 - - + -
367A ASP 3.9 4.7 - - - -
368A ALA* 4.0 10.5 - - + +
387A THR* 4.0 3.6 - - + -
388A VAL* 1.3 78.7 - - - +
390A SER* 1.3 57.8 + - - +
391A ILE* 3.5 25.1 - - + -
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Residues in contact with SER 390 (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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207A ALA 4.0 7.3 + - - -
208A ILE* 4.0 8.2 - - - +
212A THR* 3.5 21.8 - - - +
214A LEU 4.0 4.3 - - - -
215A VAL* 3.9 11.3 - - - +
365A VAL* 3.7 2.1 - - - +
366A SER* 3.4 28.4 + - - -
367A ASP* 3.0 18.6 + - - +
369A PHE* 5.2 6.1 - - - -
388A VAL* 4.0 9.4 - - - -
389A ILE* 1.3 73.0 - - - +
391A ILE* 1.3 62.1 + - - +
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Residues in contact with ILE 391 (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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91A THR* 5.2 1.6 - - + +
212A THR* 3.7 3.9 - - - -
213A VAL* 2.8 33.1 + - + -
214A LEU* 2.8 47.4 + - + +
216A LEU* 5.2 2.0 - - + -
352A LEU* 4.4 7.2 - - + -
355A ILE* 3.3 36.3 - - + -
363A LEU* 4.6 10.8 - - + -
364A TYR 3.3 11.0 - - - +
365A VAL* 3.7 15.9 - - + -
389A ILE* 3.5 29.2 - - + -
390A SER* 1.3 74.0 + - - +
392A ALA* 1.3 54.0 + - - +
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Residues in contact with ALA 392 (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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211A PHE* 3.2 24.0 - - + +
212A THR* 4.2 3.6 - - + +
213A VAL* 4.0 5.8 - - - +
363A LEU* 3.1 7.1 - - - +
364A TYR* 2.9 55.4 + - + +
366A SER* 4.3 13.6 - - - +
391A ILE* 1.3 73.5 - - - +
393A GLY* 1.3 59.4 + - - +
394A ARG 3.7 2.7 - - - -
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Residues in contact with GLY 393 (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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211A PHE* 3.4 14.4 + - - +
362A ASP* 3.0 29.6 - - - +
364A TYR* 4.0 12.1 - - - -
392A ALA* 1.3 78.6 - - - +
394A ARG* 1.3 66.5 + - - +
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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