Contacts of the helix formed by residues 337 - 345 (chain A) in PDB entry 3HF8
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 337 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181A LEU* 3.8 2.5 - - - -
257A ARG* 3.9 0.7 - - - +
263A PHE 2.8 21.2 + - - -
264A TYR* 3.8 7.6 - - - -
333A GLY 3.6 15.0 + - - -
334A LEU 3.2 2.0 + - - +
335A LEU 3.6 0.2 - - - -
336A SER* 1.3 78.6 + - - +
338A ILE* 1.3 64.6 + - - +
339A SER* 3.4 2.4 + - - -
340A GLU* 3.1 26.9 + - - +
341A LEU* 3.0 23.4 + - - +
401A ML0 3.6 16.4 - - - -
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Residues in contact with ILE 338 (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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176A THR* 4.1 4.0 - - + +
177A VAL* 3.9 21.5 - - + +
180A GLU* 3.6 37.2 - - + +
181A LEU* 3.6 26.7 - - + +
184A LEU* 3.7 10.8 - - + +
262A PRO 4.2 13.4 + - - +
263A PHE* 3.2 39.7 + - + -
336A SER 4.0 1.0 + - - -
337A SER* 1.3 72.5 - - - +
339A SER* 1.3 63.5 + - - +
342A LYS* 3.5 38.2 + - - +
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Residues in contact with SER 339 (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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263A PHE* 2.9 31.4 + - - +
264A TYR* 3.5 10.9 - - - +
337A SER* 3.4 2.3 + - - -
338A ILE* 1.3 79.6 - - - +
340A GLU* 1.3 62.0 + - - +
342A LYS* 3.5 21.4 + - - +
343A HIS* 3.1 20.6 + - - +
369A PHE* 3.7 16.3 - - - -
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Residues in contact with GLU 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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264A TYR* 4.0 12.5 - - - -
318A PHE* 3.6 15.0 - - - -
333A GLY 4.7 1.9 - - - +
334A LEU* 3.4 18.0 - - + +
337A SER* 3.1 20.7 + - - +
339A SER* 1.3 75.1 + - - +
341A LEU* 1.3 60.3 + - - +
343A HIS* 4.1 1.3 - - - -
344A ALA* 2.8 30.3 + - - +
368A THR 4.6 1.2 - - - +
369A PHE* 3.7 36.9 - - + -
370A GLN* 2.9 20.4 + - - +
373A TYR* 2.7 33.4 + - - +
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Residues in contact with LEU 341 (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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181A LEU* 3.9 15.9 - - + -
184A LEU* 3.7 30.3 - - + -
185A TYR* 4.1 18.6 - - + -
188A HIS* 3.4 30.5 - - + -
329A VAL* 3.5 43.3 - - + -
334A LEU* 3.3 17.0 + - + +
335A LEU* 4.3 5.6 - - + -
337A SER 3.0 18.5 + - - +
338A ILE 3.9 3.6 - - - +
340A GLU* 1.3 76.7 - - - +
342A LYS* 1.3 63.1 + - - +
344A ALA* 3.6 9.5 + - - +
345A LEU* 3.7 5.2 + - - +
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Residues in contact with LYS 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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184A LEU* 3.8 28.7 - - + -
188A HIS* 4.1 11.7 + - - +
338A ILE* 3.5 30.9 + - - +
339A SER* 3.8 22.3 + - - +
340A GLU 3.3 0.2 - - - -
341A LEU* 1.3 74.6 - - - +
343A HIS* 1.3 66.4 + - - +
345A LEU* 3.4 4.3 + - - +
346A SER* 3.2 23.9 + - - -
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Residues in contact with HIS 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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339A SER 3.1 15.3 + - - +
340A GLU 3.6 3.4 - - - +
342A LYS* 1.3 79.5 - - - +
344A ALA* 1.3 62.6 + - - +
346A SER* 2.6 29.6 + - - -
348A HIS* 4.2 19.5 + - + +
349A ALA* 3.6 26.2 - - + +
369A PHE* 3.5 33.3 - + + +
370A GLN 4.6 6.7 + - - -
373A TYR* 3.3 27.2 + + - -
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Residues in contact with ALA 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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320A LEU* 4.2 19.3 - - + +
327A LEU* 5.4 1.7 - - - +
329A VAL* 5.0 1.6 - - + -
334A LEU* 4.0 29.2 - - + -
340A GLU 2.8 19.6 + - - +
341A LEU* 3.8 7.2 - - - +
342A LYS 3.3 0.2 - - - -
343A HIS* 1.3 74.9 - - - +
345A LEU* 1.3 66.0 + - + +
346A SER 3.9 0.2 + - - -
347A GLY* 4.9 2.6 - - - -
349A ALA* 4.5 5.5 - - - +
351A VAL* 4.9 4.5 - - - +
373A TYR* 3.8 22.2 - - + -
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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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187A THR 4.4 4.0 - - - +
188A HIS* 3.5 59.2 - - + +
320A LEU* 4.2 13.7 - - + -
327A LEU* 3.7 45.5 - - + +
329A VAL* 3.7 17.7 - - + -
341A LEU 3.7 1.3 + - - +
342A LYS 3.4 4.1 + - - -
343A HIS 3.2 0.4 - - - -
344A ALA* 1.3 82.3 - - - +
346A SER* 1.3 62.7 + - - +
347A GLY* 3.6 5.3 + - - -
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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