Contacts of the helix formed by residues 320 - 331 (chain A) in PDB entry 5E9W
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 ASN 320 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318A THR 3.5 1.8 + - - -
319A PRO* 1.3 70.0 - - - +
321A SER* 1.3 65.4 + - - +
322A PHE* 3.2 24.8 + - - +
323A GLU* 3.2 23.1 + - + +
324A LEU* 3.0 22.5 + - - +
326A ARG* 5.5 1.2 - - - +
392A LYS* 5.1 5.4 + - - +
394A THR* 3.9 24.0 - - - +
465A SER 5.3 1.6 + - - +
466A ILE 2.7 19.0 + - - +
467A TYR 4.3 1.8 - - - -
468A LEU* 3.6 33.8 - - + +
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Residues in contact with SER 321 (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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319A PRO 3.5 5.1 + - - -
320A ASN* 1.3 73.2 + - - +
322A PHE* 1.3 67.6 + - - +
324A LEU* 3.2 4.4 + - - +
325A ILE* 2.9 36.7 + - - +
372A LEU* 3.6 34.5 - - - -
373A VAL 3.3 23.7 + - - -
374A TYR* 3.6 22.5 - - - -
375A PHE* 4.4 1.4 + - - +
468A LEU* 5.0 0.8 - - - +
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Residues in contact with PHE 322 (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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320A ASN* 3.2 16.8 + - - +
321A SER* 1.3 88.5 + - - +
323A GLU* 1.3 57.8 + - - +
325A ILE* 3.5 5.8 + - - +
326A ARG* 3.0 49.3 + - - +
374A TYR* 3.7 38.1 - + - -
375A PHE* 5.1 4.3 - - + -
376A PRO* 4.2 18.6 - - + -
392A LYS* 5.1 14.6 - - - -
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Residues in contact with GLU 323 (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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320A ASN* 3.2 26.9 + - + +
322A PHE* 1.3 76.6 - - - +
324A LEU* 1.3 66.9 + - - +
326A ARG* 2.7 36.2 + - - +
327A ARG* 2.7 71.3 + - - +
465A SER* 3.9 15.5 - - - +
466A ILE* 4.3 6.7 - - + +
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Residues in contact with LEU 324 (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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319A PRO* 3.8 16.2 - - + +
320A ASN 3.0 15.2 + - - +
321A SER* 3.2 8.3 + - - +
323A GLU* 1.3 78.6 - - - +
325A ILE* 1.3 62.7 + - - +
327A ARG* 3.5 0.4 + - - +
328A LEU* 3.2 22.0 + - - +
336A PHE* 3.7 28.5 - - + -
343A VAL* 4.3 16.2 - - + -
345A PHE* 4.4 7.5 - - + -
358A TYR* 3.6 35.2 - - + +
360A PHE* 6.1 0.7 - - + -
372A LEU* 3.8 22.4 - - + -
466A ILE* 4.1 24.9 - - + -
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Residues in contact with ILE 325 (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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321A SER* 2.9 24.1 + - - +
322A PHE* 3.9 5.4 - - - +
324A LEU* 1.3 72.9 - - - +
326A ARG* 1.3 61.2 + - - +
328A LEU* 3.1 5.2 + - + +
329A GLU* 2.8 55.7 + - - +
345A PHE* 4.4 12.1 - - + -
351A TYR* 3.6 45.1 - - + +
372A LEU* 3.9 20.0 - - + -
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Residues in contact with ARG 326 (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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320A ASN* 5.5 1.2 - - - +
322A PHE* 3.0 36.6 + - - +
323A GLU* 2.7 54.8 + - - +
324A LEU 3.3 0.4 - - - -
325A ILE* 1.3 78.6 - - - +
327A ARG* 1.3 61.9 + - + +
329A GLU* 3.5 5.1 + - - +
330A ALA* 3.0 30.5 + - + +
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Residues in contact with ARG 327 (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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323A GLU* 2.7 47.9 + - - +
325A ILE 3.3 0.2 - - - -
326A ARG* 1.3 77.4 - - + +
328A LEU* 1.3 65.7 + - - +
330A ALA* 3.4 7.2 + - - +
331A SER* 3.1 23.6 + - - -
336A PHE* 3.7 36.7 - - + +
341A TYR* 2.9 22.0 + - - -
462A GLU* 2.7 29.6 + - - +
465A SER* 2.8 29.3 + - - -
466A ILE* 3.3 19.6 - - - +
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Residues in contact with LEU 328 (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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324A LEU 3.2 13.4 + - - +
325A ILE* 3.1 10.5 + - + +
327A ARG* 1.3 76.7 - - - +
329A GLU* 1.3 57.7 + - - +
331A SER* 3.1 14.1 + - - -
333A THR 4.2 0.2 - - - +
334A GLU* 3.5 39.5 - - - +
336A PHE* 3.7 12.7 - - + -
345A PHE* 3.5 39.3 - - + -
348A LYS* 3.0 52.6 + - + -
351A TYR* 3.7 20.2 - - + +
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Residues in contact with GLU 329 (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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325A ILE* 2.8 30.9 + - - +
326A ARG* 4.2 4.9 - - - +
328A LEU* 1.3 76.9 - - + +
330A ALA* 1.3 58.5 + - - +
331A SER 3.6 4.6 + - - +
348A LYS* 4.4 12.0 + - + +
349A GLY* 5.0 2.9 + - - -
351A TYR* 3.2 32.5 + - - +
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Residues in contact with ALA 330 (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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326A ARG* 3.0 20.9 + - + +
327A ARG* 3.7 7.9 - - - +
329A GLU* 1.3 76.7 - - - +
331A SER* 1.3 60.9 + - - +
332A GLU* 4.1 5.9 + - - +
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Residues in contact with SER 331 (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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327A ARG 3.1 12.7 + - - -
328A LEU* 3.1 14.4 + - - +
329A GLU 4.0 3.5 - - - +
330A ALA* 1.3 82.6 - - - +
332A GLU* 1.3 63.5 + - - +
333A THR* 2.9 15.3 + - - -
335A SER 2.6 29.6 + - - -
336A PHE* 4.4 5.2 - - - -
348A LYS* 3.1 17.2 + - - -
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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