Contacts of the strand formed by residues 399 - 409 (chain A) in PDB entry 5NOI
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 SER 399 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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314A PRO* 4.7 1.0 - - - +
393A ALA 3.2 12.1 - - - -
394A LEU* 4.5 13.5 - - - -
398A GLY* 1.3 74.8 - - - -
400A ILE* 1.3 73.4 + - - +
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Residues in contact with ILE 400 (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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314A PRO* 3.3 40.2 - - + +
315A GLN* 3.7 26.7 - - - +
316A PHE* 3.7 31.0 - - + -
337A THR* 4.1 9.6 - - - +
345A VAL* 6.1 0.2 - - + -
391A CYS 3.8 0.5 - - - +
392A GLN* 3.4 4.7 - - - +
393A ALA* 3.2 34.7 + - + +
399A SER* 1.3 82.8 - - - +
401A LEU* 1.3 61.2 + - - +
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Residues in contact with LEU 401 (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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316A PHE* 3.5 12.3 - - - -
319A ARG* 4.6 4.7 + - - -
390A ILE* 3.9 11.2 - - + -
391A CYS 3.2 9.6 - - - +
392A GLN* 3.9 18.2 - - + +
400A ILE* 1.3 76.9 - - - +
402A ALA* 1.3 62.7 + - - +
403A LYS* 4.2 29.2 - - + +
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Residues in contact with ALA 402 (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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316A PHE* 3.4 22.9 - - + -
319A ARG* 4.1 20.0 - - + +
320A PRO* 3.9 25.0 - - + +
389A TYR 3.8 1.2 - - - +
390A ILE* 3.6 1.7 - - - -
391A CYS* 2.9 33.2 + - - -
401A LEU* 1.3 76.8 - - - +
403A LYS* 1.3 63.2 + - - +
404A ALA 4.2 0.2 + - - -
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Residues in contact with LYS 403 (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 ARG* 5.5 0.6 - - - +
320A PRO* 4.0 9.5 - - - +
321A ARG* 5.5 0.2 - - - -
322A ASP* 4.8 1.2 - - - +
350A GLU* 3.5 30.8 + - - +
388A TYR* 4.0 22.8 - - + -
389A TYR 3.5 6.1 - - - +
390A ILE* 4.3 17.3 - - + -
401A LEU* 4.2 21.4 - - + +
402A ALA* 1.3 77.2 - - - +
404A ALA* 1.3 62.0 + - - +
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Residues in contact with ALA 404 (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 PRO* 3.8 23.6 - - + -
321A ARG 3.4 28.3 - - - +
322A ASP* 3.6 5.4 - - - -
333A PHE* 4.1 10.3 - - + -
347A TRP* 5.2 1.1 - - + -
387A GLY 4.0 0.2 - - - +
388A TYR* 3.5 5.9 - - - -
389A TYR* 2.9 38.8 + - - +
402A ALA 4.2 0.2 + - - -
403A LYS* 1.3 75.4 - - - +
405A GLN* 1.3 60.2 + - - +
406A LEU 4.0 0.3 + - - -
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Residues in contact with GLN 405 (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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322A ASP* 2.9 27.6 + - + +
323A GLN 2.9 27.5 + - - +
333A PHE* 4.3 4.0 - - - -
387A GLY* 3.5 11.4 - - - +
388A TYR* 3.3 41.6 + - + -
404A ALA* 1.3 73.1 - - - +
406A LEU* 1.3 60.7 + - - +
407A GLU* 3.1 37.2 + - + +
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Residues in contact with LEU 406 (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 GLN 3.5 10.5 - - - +
325A VAL* 4.6 9.0 - - + -
331A VAL* 4.1 40.6 - - + -
333A PHE* 3.9 9.4 - - + -
378A ILE* 4.6 4.0 - - + -
381A ILE* 4.7 7.6 - - + -
385A ASP* 4.0 29.6 - - + +
386A ALA* 3.2 5.4 - - - +
387A GLY 2.7 32.7 + - - -
389A TYR* 3.8 23.6 - - + +
404A ALA 4.0 0.6 + - - -
405A GLN* 1.3 73.4 - - - +
407A GLU* 1.3 79.1 + - - +
408A VAL* 4.3 11.4 - - + -
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Residues in contact with GLU 407 (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 GLN 2.9 14.2 + - - +
324A ILE* 3.3 27.3 - - + +
325A VAL 3.0 26.9 + - - +
386A ALA* 4.2 7.7 - - - +
387A GLY* 4.9 2.4 + - - -
405A GLN* 3.1 40.8 + - + +
406A LEU* 1.3 80.9 - - - +
408A VAL* 1.3 65.2 + - - +
409A THR 4.0 0.2 + - - -
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Residues in contact with VAL 408 (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 VAL 3.6 3.4 - - - +
327A GLN* 4.0 20.4 - - + -
381A ILE* 4.1 11.4 - - + -
382A GLN 3.4 35.4 - - - +
383A ARG* 3.7 35.9 + - + +
385A ASP* 4.3 2.0 - - + -
386A ALA* 3.6 32.4 - - + +
406A LEU* 4.3 11.7 - - + -
407A GLU* 1.3 77.4 + - - +
409A THR* 1.3 63.1 + - - +
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Residues in contact with THR 409 (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 ILE* 4.5 13.9 - - + -
325A VAL* 3.1 32.9 + - - +
326A ALA* 3.4 8.3 - - + +
327A GLN* 2.8 33.9 + - - +
383A ARG* 4.8 4.7 - - - +
408A VAL* 1.3 75.5 - - - +
410A ASP* 1.3 79.7 + - - +
412A LEU* 5.4 3.5 - - - +
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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