Contacts of the strand formed by residues 323 - 332 (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 ARG 323 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235B THR* 4.8 5.1 - - - +
250B VAL* 4.9 6.1 - - - +
251B LEU* 3.0 41.3 + - + +
253B MET* 3.5 27.4 - - + -
322B PRO* 1.3 73.6 - - - +
324B PHE* 1.3 57.9 + - - +
376B VAL 3.8 3.8 - - - +
377B ASN* 4.1 21.4 + - - +
378B GLU* 3.0 44.4 + - - +
379B GLU* 5.7 0.2 + - - -
430B PRO 5.3 0.7 - - - +
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Residues in contact with PHE 324 (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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321B MET* 3.8 8.1 - - + -
322B PRO* 3.4 17.0 - - + -
323B ARG* 1.3 74.9 - - - +
325B ARG* 1.3 65.8 + - - +
326B ILE* 3.6 29.8 - - + -
374B LEU* 3.6 30.1 - - + -
375B GLU* 3.6 1.2 - - - +
376B VAL* 3.0 58.3 + - + +
409B PHE* 3.7 28.7 - + - -
411B VAL* 4.9 4.0 - - + -
427B VAL* 4.0 11.9 - - + -
430B PRO* 3.7 33.2 - - + +
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Residues in contact with ARG 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B ARG* 4.5 6.1 - - - +
324B PHE* 1.3 78.7 - - - +
326B ILE* 1.3 64.7 + - - +
327B GLU* 4.1 8.2 + - - -
373B PHE* 3.3 34.6 - - + -
374B LEU 3.2 17.5 - - - +
375B GLU* 2.7 40.8 + - + +
430B PRO 5.5 0.8 + - - -
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Residues in contact with ILE 326 (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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76B ASN* 3.6 36.3 - - + +
77B ILE 4.4 1.1 - - - +
78B PHE* 3.9 25.4 - - + +
324B PHE* 3.6 30.5 - - + -
325B ARG* 1.3 75.4 - - - +
327B GLU* 1.3 59.4 + - - +
373B PHE* 3.8 1.0 - - - -
374B LEU* 3.1 42.5 + - + +
411B VAL* 5.2 1.3 - - + -
426B ARG 4.1 12.8 - - - +
427B VAL* 3.7 28.7 - - + +
429B ASN 4.5 4.0 - - - +
430B PRO* 5.3 0.7 - - + -
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Residues in contact with GLU 327 (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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76B ASN* 5.1 5.2 - - - +
78B PHE* 5.2 0.2 - - - -
198B ARG 4.5 10.4 - - - +
199B ILE* 5.9 1.4 - - - +
200B THR* 5.1 5.7 - - - +
325B ARG* 4.1 9.4 + - - -
326B ILE* 1.3 75.1 - - - +
328B ASP* 1.3 61.6 + - - +
371B LYS* 4.0 24.1 + - - +
372B ALA 3.5 19.1 - - - +
373B PHE* 4.2 24.5 - - + +
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Residues in contact with ASP 328 (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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71B LYS* 3.1 32.0 + - - -
76B ASN* 4.0 5.6 - - + +
77B ILE* 3.2 3.8 - - - +
78B PHE* 2.8 47.9 + - + +
327B GLU* 1.3 76.9 - - - +
329B SER* 1.3 81.1 + - - +
330B PHE* 4.4 6.3 - - - -
371B LYS* 3.3 4.9 - - - +
372B ALA* 2.8 34.4 + - + +
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Residues in contact with SER 329 (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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71B LYS* 5.4 1.2 + - - -
328B ASP* 1.3 83.7 + - - +
330B PHE* 1.3 69.9 + - - +
370B HIS 3.2 15.7 - - - -
371B LYS* 3.6 24.1 - - - -
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Residues in contact with PHE 330 (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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63B PHE* 3.5 21.1 - + - -
67B LEU* 3.5 39.7 - - + -
71B LYS* 5.6 4.7 - - + +
78B PHE 4.5 6.7 - - - -
79B LEU* 3.7 33.9 - - + -
84B ILE* 4.5 0.4 - - + -
328B ASP* 4.4 7.9 - - - +
329B SER* 1.3 82.9 - - - +
331B SER* 1.3 68.0 + - - +
332B VAL* 3.9 5.1 + - + -
335B GLN* 4.9 2.0 - - + -
369B PHE* 3.7 6.8 - - - +
370B HIS* 3.1 58.8 + + + +
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Residues in contact with SER 331 (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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330B PHE* 1.3 78.2 - - - +
332B VAL* 1.3 57.4 + - - +
333B LYS* 2.9 30.7 + - - +
334B GLU* 3.4 25.3 + - - +
335B GLN* 4.6 3.8 + - - +
367B ASP* 3.7 10.4 + - - -
368B ALA 3.6 6.0 + - - -
369B PHE* 3.9 20.4 - - - -
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Residues in contact with VAL 332 (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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63B PHE* 4.0 12.3 - - + -
84B ILE* 3.8 36.3 - - + -
88B PHE* 4.6 2.2 - - + -
330B PHE* 3.9 9.2 + - + -
331B SER* 1.3 69.9 - - - +
333B LYS* 1.3 62.6 + - - +
335B GLN* 3.2 5.8 + - - +
336B LEU* 3.1 41.3 + - + +
345B PHE* 5.5 0.2 - - - -
368B ALA* 2.9 22.2 + - + +
369B PHE 4.0 6.1 - - - +
370B HIS* 3.8 28.0 - - + +
387B THR* 5.1 2.9 - - + -
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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