Contacts of the helix formed by residues 347 - 354 (chain A) in PDB entry 3S51
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 347 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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343A LEU 3.5 3.8 + - - -
344A LEU 3.2 6.9 - - - +
345A GLN 3.5 0.6 - - - -
346A GLY* 1.3 79.0 - - - +
348A LYS* 1.3 60.6 + - - +
349A PHE* 3.2 18.4 - - - -
350A LEU* 2.9 27.0 + - - +
351A GLN* 2.8 23.3 + - - +
1033A VAL* 3.6 4.0 - - - -
1094A GLU* 2.9 36.0 + - - -
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Residues in contact with LYS 348 (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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347A SER* 1.3 70.8 - - - +
349A PHE* 1.3 62.8 + - + +
351A GLN* 2.9 46.4 + - + +
352A THR* 2.9 20.0 + - - +
994A PRO* 3.7 33.1 + - - +
995A THR* 4.9 2.2 + - - +
1033A VAL 2.9 16.4 + - - +
1034A LEU* 2.8 26.8 + - - +
1035A TYR* 2.9 33.2 - - - +
1036A LYS* 4.2 3.8 - - - +
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Residues in contact with PHE 349 (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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347A SER* 3.2 18.8 - - - -
348A LYS* 1.3 75.8 - - + +
350A LEU* 1.3 65.1 + - + -
352A THR* 3.3 9.6 + - - -
353A LEU* 3.1 34.7 + - + +
1033A VAL* 3.7 21.8 - - + -
1036A LYS* 5.7 0.2 - - - +
1037A SER* 3.6 34.2 - - - +
1038A PRO* 4.2 1.6 - - + -
1091A VAL* 3.9 14.4 - - + -
1094A GLU* 3.3 48.5 - - + -
1098A LEU* 5.5 5.2 - - + -
1138A GLN* 3.2 31.2 - - + +
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Residues in contact with LEU 350 (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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343A LEU* 3.8 27.1 - - + +
344A LEU* 3.7 15.4 - - + +
347A SER* 2.9 17.0 + - - +
349A PHE* 1.3 78.7 - - + +
351A GLN* 1.3 53.1 + - - +
353A LEU* 4.5 1.6 - - + +
354A VAL* 2.6 39.1 + - + +
1094A GLU* 2.9 34.3 - - + +
1097A TRP* 3.7 31.4 - - + -
1098A LEU* 3.6 41.7 - - + -
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Residues in contact with GLN 351 (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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344A LEU* 3.3 21.9 + - + +
345A GLN* 4.1 13.3 + - - +
347A SER 2.8 27.9 + - - +
348A LYS* 2.9 40.5 + - + +
350A LEU* 1.3 76.8 - - - +
352A THR* 1.3 64.1 + - - +
354A VAL 3.0 21.7 - - - +
355A PRO* 4.7 1.7 - - - +
356A GLN* 5.1 9.4 - - - +
1034A LEU* 5.3 3.0 - - - +
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Residues in contact with THR 352 (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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348A LYS* 2.9 18.2 + - - +
349A PHE* 3.3 12.2 + - - -
351A GLN* 1.3 79.7 - - - +
353A LEU* 1.3 67.7 + - + +
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Residues in contact with LEU 353 (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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349A PHE* 3.1 24.3 + - + +
350A LEU* 4.0 2.0 - - + +
352A THR* 1.3 87.5 - - + +
354A VAL* 1.3 60.8 + - - +
355A PRO* 3.8 6.8 - - - +
1098A LEU* 3.5 43.5 - - + -
1130A LEU 4.4 2.9 - - - +
1131A ILE* 3.9 40.1 - - + +
1134A ALA* 3.5 32.8 - - + -
1135A ILE* 5.3 0.2 - - + -
1138A GLN* 6.3 2.2 - - + -
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Residues in contact with VAL 354 (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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344A LEU* 3.8 26.4 - - + +
350A LEU 2.6 21.0 + - - +
351A GLN* 3.0 19.8 - - - +
353A LEU* 1.3 81.4 - - + +
355A PRO* 1.3 82.8 - - + +
356A GLN* 3.9 0.7 + - - +
357A ARG* 6.4 0.4 - - + -
1097A TRP* 4.5 11.2 - - + -
1098A LEU* 4.7 7.4 - - + -
1101A LYS* 3.2 42.8 - - + +
1131A ILE* 5.0 5.2 - - + -
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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