Contacts of the strand formed by residues 408 - 416 (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 PRO 408 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240B PHE* 3.3 4.9 - - + -
241B TYR 3.7 9.2 - - - +
243B ALA* 3.9 23.6 - - + +
287B PRO* 4.0 14.4 - - - +
293B LEU* 3.7 26.2 - - + +
407B ARG* 1.3 92.2 - - + +
409B PHE* 1.4 60.0 - - - +
426B ARG* 5.0 0.4 - - + -
427B VAL 3.1 17.3 - - - +
428B ALA* 3.4 36.1 - - + +
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Residues in contact with PHE 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B PHE* 4.2 7.4 - + - -
284B LEU* 3.7 42.2 - - + -
285B ILE 3.3 17.7 - - - +
286B LEU* 4.2 12.8 - - + +
293B LEU* 4.0 6.2 - - - +
321B MET* 4.5 2.7 - - + -
322B PRO* 3.6 33.4 - - + -
324B PHE* 3.7 25.4 - + - -
403B PHE* 5.6 0.2 - - + -
405B ALA* 4.0 11.7 - - + -
407B ARG 3.9 11.2 - - - +
408B PRO* 1.4 73.0 - - - +
410B LEU* 1.3 66.1 + - - +
411B VAL* 4.6 2.5 - - + -
426B ARG* 3.6 1.9 - - - -
427B VAL* 3.0 54.2 + - + +
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Residues in contact with LEU 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B TYR* 3.4 29.8 - - + +
283B VAL 4.0 0.3 - - - +
284B LEU* 3.6 3.5 - - - -
285B ILE* 2.8 62.4 + - + +
293B LEU* 3.8 23.8 - - + +
296B VAL* 4.2 12.8 - - + -
297B GLU* 3.7 20.6 - - + +
300B LEU* 3.7 26.5 - - + -
409B PHE* 1.3 75.1 - - - +
411B VAL* 1.3 60.8 + - - +
412B LEU* 5.1 4.3 - - + -
424B MET* 6.0 1.3 - - + -
425B GLY 3.5 8.3 - - - +
426B ARG* 4.2 1.3 - - + -
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Residues in contact with VAL 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B PHE* 4.1 5.8 - - + -
282B MET* 3.7 28.7 - - + -
283B VAL 3.7 3.6 - - - -
284B LEU* 3.6 23.1 - - + -
324B PHE* 4.9 3.6 - - + -
326B ILE* 5.2 2.9 - - + -
374B LEU* 3.8 24.0 - - + -
409B PHE* 4.0 10.7 + - + +
410B LEU* 1.3 73.7 - - - +
412B LEU* 1.3 74.8 + - - +
413B ILE* 4.9 1.3 - - + +
424B MET* 3.5 0.7 - - - +
425B GLY* 2.8 51.1 + - - +
426B ARG* 4.6 0.4 - - - +
427B VAL* 5.2 2.2 - - + +
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Residues in contact with LEU 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B MET* 4.7 0.2 - - - -
283B VAL* 3.3 46.3 + - + +
285B ILE* 4.4 21.5 - - + -
300B LEU* 5.7 2.2 - - + -
308B TRP* 4.2 15.3 - - + +
410B LEU* 5.1 5.6 - - + -
411B VAL* 1.3 83.4 - - - +
413B ILE* 1.3 67.7 + - - +
414B ARG* 3.4 16.0 + - + +
421B ILE* 4.7 16.8 - - + -
423B PHE 3.4 8.1 - - - -
424B MET* 3.8 30.5 - - + -
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Residues in contact with ILE 413 (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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78B PHE* 4.8 2.7 - - + -
222B PHE* 3.8 22.7 - - + -
275B PHE* 4.3 3.8 - - + -
280B ILE* 3.5 19.1 - - + -
281B THR 3.4 13.7 - - - +
282B MET* 4.0 22.4 - - + +
374B LEU* 4.1 13.2 - - + -
381B SER* 4.7 2.2 - - - -
383B ALA* 3.6 30.5 - - + -
411B VAL* 4.9 1.0 - - + +
412B LEU* 1.3 72.3 - - - +
414B ARG* 1.3 63.1 + - - +
421B ILE* 4.1 0.3 - - - -
422B ILE* 3.2 3.5 + - + -
423B PHE* 2.8 55.8 + - + +
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Residues in contact with ARG 414 (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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280B ILE* 3.0 5.9 - - - +
281B THR* 2.9 41.9 + - + -
305B LEU* 4.3 15.4 - - - +
308B TRP* 3.0 72.8 - - + +
309B LEU* 5.2 1.0 - - - +
412B LEU* 3.8 15.9 - - + +
413B ILE* 1.3 77.8 - - - +
415B GLU* 1.3 64.9 + - - +
416B VAL* 3.8 6.7 + - - +
419B ASN* 3.6 43.8 + - - +
420B THR 3.2 13.6 + - - +
421B ILE* 4.0 12.7 - - + +
422B ILE* 3.8 11.0 - - - +
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Residues in contact with GLU 415 (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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130B ARG 4.9 5.0 - - - +
131B LEU* 4.5 20.8 - - + +
133B ARG* 5.0 4.3 + - - -
141B LEU* 5.2 2.7 - - + -
279B ASP* 3.1 35.7 - - + +
280B ILE* 4.1 12.8 - - + -
414B ARG* 1.3 71.8 - - - +
416B VAL* 1.3 61.8 + - - +
417B ALA* 3.2 7.8 + - - +
418B LEU* 3.2 35.2 + - - +
419B ASN* 3.0 8.8 + - - -
420B THR* 3.0 45.2 + - - -
422B ILE* 3.8 13.2 - - + +
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Residues in contact with VAL 416 (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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260B ARG* 5.1 8.5 - - - +
272B GLU* 4.5 3.6 - - - +
278B ASP 4.1 10.8 - - - +
279B ASP 3.0 27.9 + - - +
280B ILE 4.8 0.2 - - - -
281B THR* 4.2 24.7 - - - +
308B TRP* 3.6 23.6 - - + -
414B ARG* 3.8 9.7 + - - +
415B GLU* 1.3 70.7 - - - +
417B ALA* 1.3 58.2 + - + +
418B LEU 3.0 0.2 + - - -
419B ASN* 2.8 24.9 + - - +
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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