Contacts of the strand formed by residues 408 - 414 (chain B) in PDB entry 1ATH
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 408 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391A ALA* 4.5 6.3 - - + -
392A GLY* 4.2 31.4 - - - +
283B LEU* 3.6 35.0 - - + -
284B ILE 3.4 12.8 - - - +
285B LEU* 4.2 14.1 - - + -
286B PRO* 4.9 1.8 - - + -
320B MET* 4.9 2.9 - - + -
321B PRO* 4.3 13.7 - - + -
323B PHE* 4.2 16.2 - + - -
406B ARG 4.6 0.7 - - - -
407B PRO* 1.3 74.2 - - - +
409B LEU* 1.3 83.9 + - - +
410B VAL* 4.6 4.0 - - + -
425B ARG* 3.5 4.2 - - - +
426B VAL* 3.0 71.0 + - + +
427B ALA 5.8 0.7 - - - -
429B PRO* 5.6 0.4 - - + -
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Residues in contact with LEU 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B TYR* 4.6 12.8 - - + +
283B LEU* 3.3 5.9 - - - -
284B ILE* 2.9 48.8 + - + +
286B PRO* 6.2 2.0 - - + -
292B LEU 5.5 1.6 - - - +
295B VAL* 4.4 23.1 - - + -
296B GLU* 4.4 26.0 - - + +
299B LEU* 4.5 12.3 - - + -
307B TRP* 5.8 1.1 - - + -
407B PRO 5.5 1.1 - - - +
408B PHE* 1.3 85.3 - - - +
410B VAL* 1.3 60.2 + - - +
411B PHE* 3.7 31.2 - - + -
424B GLY 3.5 10.3 - - - +
425B ARG* 4.8 4.7 - - + -
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Residues in contact with VAL 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B PHE* 4.6 3.4 - - + -
281B MET* 3.7 35.2 - - + -
282B VAL 3.4 4.7 - - - +
283B LEU* 4.5 7.4 - - + +
323B PHE* 5.9 1.6 - - + -
373B LEU* 4.4 18.6 - - + -
408B PHE* 4.6 2.5 - - + -
409B LEU* 1.3 74.3 - - - +
411B PHE* 1.3 73.5 + - - +
412B ILE* 4.3 7.2 - - + -
423B MET* 3.6 0.8 - - - -
424B GLY* 2.9 48.1 + - - +
425B ARG 4.3 0.2 - - - +
426B VAL* 3.8 26.5 - - + -
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Residues in contact with PHE 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B THR* 5.6 0.2 - - + -
280B THR 3.8 0.2 - - - +
281B MET* 3.3 4.0 - - - +
282B VAL* 2.9 50.0 + - + +
284B ILE* 4.2 13.0 - - + -
299B LEU* 3.6 33.2 - - + -
304B LEU* 3.6 40.6 - - + -
307B TRP* 5.8 0.2 - + - -
409B LEU* 3.7 30.3 - - + -
410B VAL* 1.3 82.8 - - - +
412B ILE* 1.3 65.5 + - - +
413B ARG* 3.8 7.1 + - + +
420B ILE* 4.3 12.3 - - + -
422B PHE 3.7 7.0 - - - +
423B MET* 4.4 23.6 - - + -
424B GLY 5.1 0.2 - - - -
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Residues in contact with ILE 412 (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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77B PHE* 4.8 2.2 - - + -
221B PHE* 4.1 22.7 - - + -
274B PHE* 4.5 2.2 - - + -
279B ILE* 3.9 20.6 - - + -
280B THR 3.2 11.4 - - - +
281B MET* 3.7 31.9 - - + -
373B LEU* 3.9 20.2 - - + -
380B SER* 4.7 0.4 - - - +
382B ALA* 4.8 3.4 - - + -
410B VAL* 4.3 6.7 - - + -
411B PHE* 1.3 76.7 - - - +
413B ARG* 1.3 57.9 + - - +
420B ILE* 4.1 1.0 - - - -
421B ILE* 3.2 36.1 + - + +
422B PHE* 2.9 35.0 + - + +
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Residues in contact with ARG 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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56B SER* 5.5 0.6 + - - -
279B ILE* 3.3 4.9 - - - +
280B THR* 2.9 48.5 + - + -
282B VAL* 4.2 11.7 - - + -
304B LEU* 3.4 31.6 - - - +
305B GLN* 6.3 1.0 - - - +
308B LEU* 3.6 30.2 - - - +
411B PHE* 3.8 9.5 + - + +
412B ILE* 1.3 76.2 - - - +
414B GLU* 1.3 59.4 + - - +
415B VAL* 3.8 14.7 + - + +
418B ASN* 3.4 41.3 + - - +
419B THR 3.5 8.3 - - - +
420B ILE* 3.4 30.5 - - + +
421B ILE* 5.4 1.3 - - - -
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Residues in contact with GLU 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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129B ARG 4.3 1.7 - - - +
130B LEU* 3.9 14.1 - - + -
132B ARG* 2.8 33.6 + - - +
140B LEU* 5.0 2.2 - - + -
278B ASP* 3.2 17.6 - - + +
279B ILE* 4.3 10.1 - - + +
413B ARG* 1.3 71.2 - - - +
415B VAL* 1.3 63.5 + - - +
416B PRO* 3.6 15.2 - - - +
417B LEU* 3.1 42.2 + - - +
418B ASN* 3.1 14.2 + - - -
419B THR* 3.0 20.5 + - - +
421B ILE* 4.7 6.0 - - + +
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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