Contacts of the strand formed by residues 399 - 405 (chain A) in PDB entry 3S95
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 399 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331A HIS* 3.5 49.0 + + - +
385A VAL* 4.4 15.0 - - + -
388A MET* 3.7 42.4 + - + +
389A ARG* 4.1 23.1 - - + -
391A LEU 5.6 2.0 + - - +
392A GLU* 5.4 0.9 - - - +
397A LEU 3.7 3.4 + - - -
398A LYS* 1.3 88.2 + - - +
400A ILE* 1.3 60.3 + - - +
401A GLY* 3.5 28.3 - - - -
402A VAL* 3.7 17.7 - - + -
411A PHE* 3.7 33.4 - + + -
412A ILE 3.9 3.8 - - - -
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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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330A PRO 4.4 1.9 - - - +
331A HIS* 3.4 8.6 - - - -
332A ARG* 3.1 48.4 + - - +
334A PHE* 4.1 10.1 - - + -
363A GLU* 5.5 1.3 - - - +
365A MET* 3.8 28.7 - - + -
398A LYS* 4.1 15.3 - - + +
399A PHE* 1.3 79.8 - - - +
401A GLY* 1.3 59.9 + - - +
412A ILE* 2.8 14.7 + - + +
413A THR 3.6 7.6 - - - +
414A GLU* 3.5 34.3 - - + +
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Residues in contact with GLY 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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331A HIS* 4.6 2.0 - - - -
332A ARG 3.0 15.5 - - - -
334A PHE* 4.6 3.4 - - - -
399A PHE* 3.5 16.1 - - - -
400A ILE* 1.3 81.9 - - - +
402A VAL* 1.3 69.7 + - - +
411A PHE* 3.5 2.3 - - - -
412A ILE* 2.8 29.3 + - - +
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Residues in contact with VAL 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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332A ARG 3.0 7.8 + - - +
333A ILE* 3.4 31.4 - - + -
334A PHE* 2.9 27.7 + - - -
385A VAL* 5.5 0.4 - - + -
389A ARG* 3.8 21.8 - - - +
399A PHE* 3.7 19.7 - - + -
401A GLY* 1.3 79.1 - - - +
403A LEU* 1.3 63.3 + - - +
404A TYR* 4.4 9.4 - - + -
409A LEU* 3.7 24.2 - - + -
410A ASN 3.4 6.1 - - - +
411A PHE* 4.3 2.0 - - + +
412A ILE* 4.4 3.6 - - - +
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Residues in contact with LEU 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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333A ILE* 4.8 0.9 - - - -
334A PHE* 3.5 18.4 - - + +
335A ARG 3.9 15.0 - - - +
336A PRO* 3.9 15.7 - - + -
339A LEU* 3.3 33.4 - - + -
341A HIS* 6.0 1.1 - - + -
367A MET* 4.2 8.1 - - - -
402A VAL* 1.3 77.2 - - - +
404A TYR* 1.3 65.3 + - - +
405A LYS* 3.6 34.5 - - + -
408A ARG 3.6 0.2 - - - +
409A LEU* 3.7 1.4 - - - -
410A ASN* 2.7 55.1 + - + +
412A ILE* 4.6 4.9 - - + -
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Residues in contact with TYR 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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333A ILE* 4.1 21.2 - - + +
334A PHE 4.4 2.6 + - - -
336A PRO* 3.6 20.3 - - - +
402A VAL* 4.4 11.2 - - + -
403A LEU* 1.3 75.6 - - - +
405A LYS* 1.3 60.9 + - - +
406A ASP 3.9 1.5 + - - -
407A LYS* 3.7 23.6 - - - +
408A ARG 3.2 17.0 - - - -
409A LEU* 3.6 45.4 - - + +
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Residues in contact with LYS 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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336A PRO* 3.9 24.0 - - + -
341A HIS* 3.2 31.8 + - - -
367A MET* 3.8 2.6 - - - +
369A GLU* 2.7 31.9 + - - +
403A LEU* 3.6 21.2 + - + -
404A TYR* 1.3 69.2 - - - +
406A ASP* 1.3 76.3 + - - +
407A LYS 3.3 0.2 - - - -
408A ARG* 2.9 49.2 + - + +
410A ASN* 3.7 12.1 - - - +
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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