Contacts of the helix formed by residues 424 - 429 (chain L) in PDB entry 4DVQ
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 ASN 424 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302B GLU* 6.0 1.6 - - - +
336L VAL* 5.0 5.6 - - - +
371L GLU* 2.9 21.3 + - - +
422L ARG* 4.7 8.4 - - + +
423L TYR* 1.3 74.6 - - - +
425L PRO* 1.3 71.3 - - - +
426L GLN* 3.2 39.0 + - - +
427L ARG* 3.3 34.4 + - - +
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Residues in contact with PRO 425 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336L VAL* 3.7 34.3 - - + -
340L LEU* 5.2 4.0 - - + -
364L LEU* 4.2 11.2 - - + +
367L ALA* 3.4 39.4 - - + +
368L ALA* 4.0 22.4 - - + +
371L GLU* 4.8 0.9 - - + -
423L TYR* 4.1 8.7 - - + -
424L ASN* 1.3 91.8 - - - +
426L GLN* 1.3 60.3 + - - +
427L ARG 3.1 2.2 + - - -
428L TRP* 3.2 14.2 + - + -
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Residues in contact with GLN 426 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B LYS* 5.6 0.2 + - - -
300B SER* 3.5 23.5 + - - -
301B LEU* 3.2 40.0 + - - +
302B GLU* 3.7 9.1 - - - +
364L LEU* 6.4 1.8 - - - -
424L ASN* 3.2 33.1 + - - +
425L PRO* 1.3 73.3 - - - +
427L ARG* 1.3 60.8 + - - +
428L TRP* 3.0 7.3 + - - -
429L LEU* 3.5 35.0 + - + +
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Residues in contact with ARG 427 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B LYS* 4.6 21.7 + - - +
300B SER* 5.7 0.7 - - - -
371L GLU* 2.8 29.0 + - - -
374L ARG* 3.3 16.9 - - - +
417L PHE* 3.7 29.9 - - + +
418L PRO* 2.9 26.3 + - - +
419L ARG 2.8 27.3 + - - -
420L PRO 3.7 1.4 + - - -
422L ARG* 3.2 23.0 + - - +
424L ASN* 3.3 23.0 + - + +
425L PRO 3.1 0.6 - - - -
426L GLN* 1.3 79.8 - - - +
428L TRP* 1.3 73.8 + - + +
429L LEU 3.6 2.0 + - - -
430L ASP* 4.7 4.7 - - - +
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Residues in contact with TRP 428 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367L ALA* 3.6 24.6 - - + +
370L LYS* 3.9 39.0 - - + -
371L GLU* 2.9 35.1 + - - +
374L ARG* 3.8 17.7 - - + -
417L PHE* 3.6 30.5 - + - -
425L PRO* 3.2 20.8 + - + +
426L GLN 3.0 2.8 - - - -
427L ARG* 1.3 89.2 - - + +
429L LEU* 1.3 57.2 + - - +
430L ASP* 3.1 16.6 + - - +
440L HIS* 3.6 37.0 - - + -
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Residues in contact with LEU 429 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B PHE* 3.0 22.3 - - + -
297B ALA 5.1 6.7 - - - +
298B GLU* 4.0 18.6 - - - +
299B LEU 4.1 2.0 - - - +
300B SER* 3.8 30.7 - - - +
364L LEU* 5.3 13.2 - - + -
426L GLN* 3.5 31.9 + - + +
427L ARG 3.6 2.6 + - - -
428L TRP* 1.3 72.9 - - - +
430L ASP* 1.3 70.5 + - - +
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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