Contacts of the helix formed by residues 333 - 342 (chain A) in PDB entry 4DN5
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 VAL 333 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332A SER* 1.3 73.5 + - - +
334A GLU* 1.3 66.0 + - + +
336A TYR* 3.6 9.7 + - + +
337A LEU* 3.1 29.5 + - + +
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Residues in contact with GLU 334 (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 SER* 4.0 4.8 + - - +
333A VAL* 1.3 80.4 - - + +
335A GLU* 1.3 58.6 + - + +
336A TYR 3.2 1.8 - - - -
337A LEU* 3.1 11.2 + - + +
338A VAL* 2.8 42.4 + - + +
355A SER* 3.9 32.3 + - - +
358A LYS* 4.2 21.2 + - - +
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Residues in contact with GLU 335 (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 SER* 3.6 30.2 + - - +
333A VAL 3.5 0.4 - - - -
334A GLU* 1.3 76.5 - - + +
336A TYR* 1.3 59.8 + - - +
338A VAL* 4.0 8.8 - - - +
339A HIS* 3.5 19.6 + - - +
342A GLN* 5.6 0.2 + - - -
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Residues in contact with TYR 336 (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 SER 3.5 18.4 + - - +
333A VAL* 3.6 10.0 + - + +
334A GLU 3.2 0.2 - - - -
335A GLU* 1.3 79.2 - - - +
337A LEU* 1.3 68.3 + - + +
338A VAL 3.3 0.2 - - - -
339A HIS* 3.5 10.6 + - + +
340A ALA* 3.4 21.9 + - + +
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Residues in contact with LEU 337 (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 VAL* 3.1 20.2 + - + +
334A GLU* 3.1 14.3 + - + +
336A TYR* 1.3 78.8 - - + +
338A VAL* 1.3 65.6 + - - +
340A ALA* 3.3 20.3 + - - +
341A LEU* 3.5 27.8 + - + +
351A HIS* 4.8 19.3 - - + +
352A SER* 4.9 10.3 - - - +
355A SER* 4.7 15.0 - - - +
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Residues in contact with VAL 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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334A GLU* 2.8 25.5 + - + +
335A GLU* 4.1 8.3 - - - +
336A TYR 3.3 0.2 - - - -
337A LEU* 1.3 77.5 - - + +
339A HIS* 1.3 56.6 + - - +
341A LEU* 3.0 25.6 + - + +
342A GLN* 3.1 34.2 + - + +
355A SER* 3.7 39.3 - - - +
356A LEU* 4.4 5.4 - - + +
359A THR* 3.6 25.1 - - + +
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Residues in contact with HIS 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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335A GLU 3.5 15.8 + - - +
336A TYR* 3.5 12.7 + - + +
337A LEU 3.3 0.8 - - - -
338A VAL* 1.3 78.6 - - - +
340A ALA* 1.3 59.8 + - - +
341A LEU 3.4 0.3 + - - -
342A GLN* 3.5 35.1 + - + +
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Residues in contact with ALA 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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336A TYR* 3.4 12.7 + - + +
337A LEU* 3.3 12.7 + - - +
338A VAL 3.2 0.4 - - - -
339A HIS* 1.3 79.9 + - - +
341A LEU* 1.3 62.3 + - + +
342A GLN 4.4 2.9 - - - +
344A SER* 5.0 6.2 + - - -
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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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337A LEU* 3.7 32.5 - - + +
338A VAL* 3.0 12.6 + - - +
340A ALA* 1.3 79.6 - - + +
342A GLN* 1.3 60.5 - - - +
344A SER* 3.0 29.8 + - - +
346A SER* 3.7 24.3 + - - +
352A SER* 3.5 36.6 - - - +
356A LEU* 4.2 21.3 - - + +
378A GLU* 4.4 1.9 - - - +
380A VAL* 4.3 10.3 - - + -
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Residues in contact with GLN 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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335A GLU 5.6 0.2 + - - -
338A VAL* 3.1 29.2 + - + +
339A HIS* 3.5 37.1 + - + +
340A ALA 3.4 3.4 - - - +
341A LEU* 1.3 77.7 - - - +
343A GLY* 1.3 61.2 + - - +
344A SER* 3.3 4.3 + - - -
356A LEU* 3.8 15.7 - - + -
359A THR* 4.8 11.5 + - - +
363A ARG* 5.5 5.9 + - - -
378A GLU* 3.3 15.2 - - - +
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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