Contacts of the helix formed by residues 333 - 347 (chain I) 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 333 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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329I GLU* 2.9 37.8 + - - +
330I LEU* 3.3 6.6 - - - +
331I ALA 3.2 1.2 - - - -
332I ARG* 1.3 83.1 + - - +
334I PRO* 1.3 68.3 - - - +
335I ASP* 3.1 10.2 + - - +
336I VAL* 3.0 28.6 + - + +
337I GLN 3.1 8.8 + - - -
422I ARG* 6.0 2.8 - - - +
423I TYR* 3.6 30.0 + - + +
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Residues in contact with PRO 334 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280H PHE* 6.2 4.0 - - + -
330I LEU 3.6 7.6 - - - +
331I ALA 3.7 9.2 - - - +
332I ARG 3.4 9.4 - - - +
333I ASN* 1.3 88.2 - - - +
335I ASP* 1.3 64.0 + - - +
337I GLN* 3.1 9.3 + - + +
338I GLN* 2.9 32.6 + - - +
341I ARG* 5.0 1.4 + - - -
473I VAL 6.0 0.9 - - - +
478I GLN* 5.6 2.5 - - - +
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Residues in contact with ASP 335 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333I ASN* 3.9 10.6 + - - +
334I PRO* 1.3 83.6 - - - +
336I VAL* 1.3 65.9 + - + +
338I GLN* 3.3 13.4 - - - +
339I ILE* 3.2 29.0 + - + +
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Residues in contact with VAL 336 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330I LEU* 4.6 6.1 - - + -
333I ASN* 3.0 26.1 + - + +
335I ASP* 1.3 79.4 - - + +
337I GLN* 1.3 60.6 + - - +
339I ILE* 3.4 9.4 + - + +
340I LEU* 2.9 40.4 + - + +
364I LEU* 5.4 2.5 - - + -
423I TYR* 4.1 16.4 - - + +
424I ASN* 5.6 1.1 - - - +
425I PRO* 3.7 33.0 - - + -
426I GLN* 4.7 11.9 - - - +
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Residues in contact with GLN 337 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330I LEU* 2.8 38.7 - - + +
333I ASN 3.1 4.8 + - - -
334I PRO* 3.1 13.4 + - - +
336I VAL* 1.3 77.8 - - - +
338I GLN* 1.3 51.1 + - - +
340I LEU* 3.1 12.1 + - - +
341I ARG* 2.8 69.2 + - - +
468I LEU* 3.6 12.8 - - + +
472I LEU* 3.6 3.0 - - - +
473I VAL* 2.8 53.1 - - - +
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Residues in contact with GLN 338 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334I PRO* 2.9 12.3 + - - +
335I ASP* 3.3 16.1 - - - +
337I GLN* 1.3 75.6 - - - +
339I ILE* 1.3 63.9 + - + +
341I ARG* 3.0 22.7 + - - +
342I GLN* 2.9 37.2 + - + +
472I LEU* 6.0 2.2 - - - +
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Residues in contact with ILE 339 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335I ASP* 3.2 16.1 + - + +
336I VAL* 3.9 10.1 - - + +
337I GLN 3.3 0.2 - - - -
338I GLN* 1.3 81.7 - - + +
340I LEU* 1.3 63.9 + - - +
341I ARG 3.2 0.5 + - - -
342I GLN* 3.3 19.7 + - + +
343I GLU* 3.4 13.5 + - + +
364I LEU* 4.0 29.6 - - + -
426I GLN* 5.2 15.0 - - + +
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Residues in contact with LEU 340 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330I LEU* 3.5 35.0 - - + -
336I VAL* 2.9 27.2 + - + +
337I GLN 3.5 4.5 - - - +
339I ILE* 1.3 76.5 - - - +
341I ARG* 1.3 60.7 + - - +
343I GLU* 3.3 9.6 - - - +
344I SER* 3.1 23.4 + - - -
364I LEU* 3.0 48.5 - - + +
365I LEU* 3.5 33.7 - - + +
368I ALA* 4.2 8.5 - - + -
468I LEU* 3.7 14.9 - - + +
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Residues in contact with ARG 341 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334I PRO 5.0 0.8 + - - -
337I GLN* 2.8 45.7 + - - +
338I GLN* 3.0 30.1 + - - +
340I LEU* 1.3 73.8 - - - +
342I GLN* 1.3 59.0 + - + +
343I GLU 3.0 1.3 - - - -
344I SER* 2.9 7.4 + - - -
345I LEU* 2.7 51.5 + - + +
468I LEU* 3.0 40.9 + - + +
471I PHE 3.1 15.2 + - - -
472I LEU* 3.3 27.3 - - - +
502I ILE* 3.4 21.0 - - - +
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Residues in contact with GLN 342 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338I GLN* 2.9 25.7 + - + +
339I ILE* 3.3 15.7 + - + +
341I ARG* 1.3 75.9 - - + +
343I GLU* 1.3 56.6 + - - +
345I LEU* 4.1 9.9 - - + +
346I ALA* 3.1 25.7 + - - +
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Residues in contact with GLU 343 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339I ILE* 3.4 8.0 + - + +
340I LEU* 3.3 21.1 - - + +
341I ARG 3.0 1.2 - - - -
342I GLN* 1.3 77.6 - - - +
344I SER* 1.3 63.5 + - - +
346I ALA* 3.1 20.5 - - + +
347I ALA* 3.3 11.4 + - - +
361I GLU 3.0 23.1 - - - +
362I LEU* 3.0 25.4 - - + +
363I PRO* 3.4 6.5 - - - +
364I LEU* 3.0 43.0 + - + +
365I LEU* 3.7 4.5 + - + -
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Residues in contact with SER 344 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340I LEU 3.1 16.4 + - - -
341I ARG* 2.9 8.8 + - - -
343I GLU* 1.3 73.5 - - - +
345I LEU* 1.3 65.8 + - - +
347I ALA 3.3 1.2 + - - -
348I ALA* 3.2 18.2 + - - +
362I LEU* 3.8 9.3 - - - +
365I LEU* 4.9 2.4 - - - +
465I HIS* 2.7 56.4 + - - -
468I LEU* 4.2 11.4 - - - +
469I LYS* 4.2 7.5 - - - +
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Residues in contact with LEU 345 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341I ARG* 2.7 42.5 + - + +
342I GLN* 4.1 8.5 - - + +
344I SER* 1.3 72.6 - - - +
346I ALA* 1.3 62.6 + - - +
347I ALA 2.9 1.7 + - - -
348I ALA* 3.0 22.4 + - + +
349I ALA 4.8 0.2 + - - -
469I LYS* 3.9 33.9 - - + +
502I ILE* 5.7 3.1 - - + -
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Residues in contact with ALA 346 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342I GLN 3.1 18.2 + - - +
343I GLU* 3.1 19.5 - - + +
345I LEU* 1.3 76.3 - - - +
347I ALA* 1.3 55.8 + - + +
349I ALA* 5.3 2.6 + - - +
350I SER* 4.6 1.7 + - - -
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Residues in contact with ALA 347 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343I GLU 3.3 12.7 + - - +
344I SER 3.3 2.9 + - - +
345I LEU 3.1 0.8 - - - -
346I ALA* 1.3 77.1 - - + +
348I ALA* 1.3 64.8 + - - +
349I ALA 3.3 2.7 - - - -
350I SER* 3.1 16.5 + - - +
351I ILE* 2.9 44.2 + - + +
361I GLU* 4.0 23.3 - - + +
362I LEU* 4.5 3.1 - - + -
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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