Contacts of the strand formed by residues 339 - 346 (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 LEU 339 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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334A PHE* 4.5 8.1 - - + -
335A ARG 4.4 0.2 - - - +
336A PRO 3.2 11.8 + - - +
337A SER 3.2 3.7 - - - +
338A ASP* 1.3 90.9 - - + +
340A ILE* 1.3 61.4 + - - +
341A HIS* 3.3 17.6 + - + -
356A VAL* 4.1 25.4 - - + -
357A THR 3.5 2.7 - - - +
358A HIS* 4.1 18.2 - - + +
365A MET* 4.1 25.1 - - + -
367A MET* 4.6 2.7 - - - -
403A LEU* 3.3 32.1 - - + -
412A ILE* 3.9 22.2 - - + -
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Residues in contact with ILE 340 (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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339A LEU* 1.3 71.6 - - - +
341A HIS* 1.3 72.7 + - - +
342A GLY* 3.6 0.7 + - - -
356A VAL* 3.4 3.6 - - - -
357A THR* 2.8 48.0 + - + +
358A HIS 5.2 0.2 - - - -
359A ARG* 4.2 31.9 - - + +
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Residues in contact with HIS 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A PRO* 4.7 7.0 - - + -
339A LEU* 3.3 26.2 + - + -
340A ILE* 1.3 81.3 - - - +
342A GLY* 1.3 62.2 + - - +
354A ILE* 4.6 14.1 - - + -
355A LYS 3.9 3.8 - - - -
356A VAL* 4.2 7.3 - - + +
367A MET* 3.7 19.9 - - + +
369A GLU* 5.5 0.4 - - - -
403A LEU* 6.0 0.4 - - + -
405A LYS* 3.2 32.6 + - - -
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Residues in contact with GLY 342 (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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340A ILE 3.6 1.6 + - - -
341A HIS* 1.3 75.6 - - - +
343A GLU* 1.3 73.3 + - - -
344A VAL* 3.6 2.8 + - - +
354A ILE* 3.6 8.5 - - - +
355A LYS* 2.7 21.9 + - - -
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Residues in contact with GLU 343 (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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342A GLY* 1.3 75.9 - - - +
344A VAL* 1.3 69.1 - - - +
345A LEU* 3.4 12.3 + - + +
354A ILE* 3.6 0.4 - - - -
355A LYS* 2.9 64.8 + - - +
415A TYR* 4.6 2.1 + - - -
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Residues in contact with VAL 344 (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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342A GLY 3.6 3.3 + - - +
343A GLU* 1.3 77.6 - - - +
345A LEU* 1.3 62.6 + - - +
346A GLY* 3.5 25.4 - - - +
347A LYS* 4.3 7.9 - - + -
352A GLN* 4.1 25.4 - - + +
353A ALA 3.8 5.8 - - - +
354A ILE* 4.4 13.0 - - + +
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Residues in contact with LEU 345 (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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1A STU 3.6 65.7 - - + +
343A GLU* 4.0 27.1 - - + +
344A VAL* 1.3 76.7 - - - +
346A GLY* 1.3 54.6 + - - +
353A ALA 2.7 14.9 + - - +
355A LYS* 3.9 17.9 - - + +
366A VAL* 3.5 37.0 - - + -
415A TYR* 4.0 13.9 - - + +
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Residues in contact with GLY 346 (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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1A STU 3.4 26.9 + - - -
344A VAL* 3.5 4.4 - - - +
345A LEU* 1.3 80.1 - - - +
347A LYS* 1.3 60.5 + - - -
352A GLN* 3.3 4.8 - - - +
353A ALA* 2.9 28.9 + - - +
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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