Contacts of the helix formed by residues 332 - 345 (chain i) in PDB entry 5GAG
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 332 (chain i).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330i ASP* 3.2 4.4 + - + +
331i LEU* 1.3 76.3 - - - +
333i ASP* 1.3 66.8 + - - +
334i PHE 3.3 0.2 - - - -
335i LEU* 3.2 16.3 - - + +
336i GLU* 3.0 38.3 + - - +
385i MET* 4.0 19.0 + - - +
388i ARG* 3.3 29.1 + - - +
389i ALA* 3.6 31.7 - - - +
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Residues in contact with ASP 333 (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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328i GLY 3.1 24.4 - - - +
329i PHE* 3.7 16.2 - - + -
330i ASP* 3.3 31.5 + - - +
332i ASN* 1.3 81.1 - - - +
334i PHE* 1.3 58.3 + - - +
336i GLU* 3.6 17.2 + - - +
337i GLN* 2.9 28.2 + - - +
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Residues in contact with PHE 334 (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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329i PHE* 3.7 11.4 - + + -
330i ASP 2.9 17.3 + - - +
331i LEU* 3.6 29.8 - - + -
333i ASP* 1.3 75.9 - - - +
335i LEU* 1.3 58.2 + - - +
336i GLU 3.3 0.2 - - - -
337i GLN* 3.6 23.3 - - + +
338i LEU* 2.9 64.0 + - + +
341i MET* 5.9 1.6 - - + -
376i MET* 4.2 18.2 - - + -
380i ILE* 3.9 9.9 - - + -
416i LEU 5.1 2.5 - - - -
419i GLN 4.8 0.7 - - - -
420i PHE* 3.9 31.6 - + + -
423i MET* 4.2 24.0 - - + -
37k LEU* 4.9 2.9 - - + -
41k LEU* 5.2 3.8 - - + -
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Residues in contact with LEU 335 (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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331i LEU 2.9 20.6 + - - +
332i ASN* 3.2 25.5 + - + +
334i PHE* 1.3 76.1 - - - +
336i GLU* 1.3 60.4 + - + +
338i LEU* 3.2 2.0 + - - +
339i ARG* 2.9 54.0 + - - +
377i GLU* 3.4 27.5 - - - +
380i ILE* 3.6 21.1 - - + +
381i ASN* 3.7 7.2 - - - +
385i MET* 5.8 1.1 - - - -
388i ARG* 3.5 30.3 - - - +
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Residues in contact with GLU 336 (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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332i ASN* 3.0 29.9 + - - +
333i ASP* 3.8 18.2 - - - +
335i LEU* 1.3 75.3 - - + +
337i GLN* 1.3 65.4 + - - +
338i LEU 3.1 1.1 - - - -
339i ARG* 3.8 31.9 + - - +
340i GLN* 3.0 32.8 + - - +
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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
----------------------------------------------------------
329i PHE* 3.7 22.5 - - - -
333i ASP 2.9 15.5 + - - +
334i PHE* 3.6 27.1 - - + +
336i GLU* 1.3 75.4 - - - +
338i LEU* 1.3 56.2 + - - +
340i GLN* 3.9 5.4 - - - +
341i MET* 2.9 40.5 + - - +
427i MET* 4.5 13.9 - - - +
33k ALA* 4.6 8.0 - - + +
37k LEU* 3.3 39.9 - - + +
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Residues in contact with LEU 338 (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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334i PHE* 2.9 43.4 + - + +
335i LEU* 3.6 4.9 - - - +
336i GLU 3.1 0.2 - - - -
337i GLN* 1.3 76.5 - - - +
339i ARG* 1.3 58.2 + - - +
340i GLN 3.3 1.8 - - - -
341i MET* 3.9 18.8 - - + +
342i LYS* 3.0 32.2 + - - +
373i LEU* 3.7 22.2 - - + +
376i MET* 3.5 46.2 - - + -
377i GLU* 3.7 9.9 - - + +
380i ILE* 3.4 25.1 - - + -
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Residues in contact with ARG 339 (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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335i LEU* 2.9 39.9 + - - +
336i GLU* 3.8 32.4 + - - +
338i LEU* 1.3 72.1 - - - +
340i GLN* 1.3 62.0 + - + +
342i LYS* 4.0 16.9 - - - +
343i ASN* 4.0 16.5 + - - +
377i GLU* 3.5 27.4 - - - +
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Residues in contact with GLN 340 (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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336i GLU* 3.0 22.8 + - - +
337i GLN* 3.9 6.1 - - - +
339i ARG* 1.3 79.6 - - + +
341i MET* 1.3 59.6 + - + +
342i LYS 3.5 0.2 - - - -
343i ASN* 3.5 10.1 - - - +
344i MET* 3.1 50.0 - - + +
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Residues in contact with MET 341 (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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334i PHE* 5.9 1.6 - - + -
337i GLN* 2.9 34.0 + - + +
338i LEU* 3.6 22.2 + - + +
340i GLN* 1.3 74.6 - - + +
342i LYS* 1.3 58.0 + - - +
343i ASN 3.3 2.0 - - - -
344i MET* 3.9 6.7 - - - -
345i GLY* 3.2 26.7 + - - -
373i LEU* 3.6 16.5 - - + +
34k LEU* 3.8 25.1 - - + +
37k LEU* 3.7 41.5 - - + -
38k LEU* 4.8 17.4 - - + +
41k LEU* 4.4 17.7 - - + -
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Residues in contact with LYS 342 (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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481 G 4.6 9.5 + - - -
491 G 5.5 4.8 + - - -
338i LEU 3.0 20.4 + - - +
339i ARG* 4.0 14.4 - - - +
340i GLN 3.5 0.2 - - - -
341i MET* 1.3 74.4 - - - +
343i ASN* 1.3 65.3 + - - +
345i GLY* 4.5 4.6 + - - +
370i ASP* 5.1 6.2 - - - +
373i LEU* 3.6 44.6 + - + +
374i VAL* 5.1 12.2 - - + +
377i GLU* 3.1 36.9 - - + +
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Residues in contact with ASN 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 ARG 4.0 11.6 + - - +
340i GLN* 3.5 13.7 + - - +
342i LYS* 1.3 83.8 - - + +
344i MET* 1.3 66.6 + - + +
345i GLY 3.8 1.2 + - - +
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Residues in contact with MET 344 (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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340i GLN* 3.1 48.9 - - + +
341i MET* 3.9 7.4 - - - +
343i ASN* 1.3 80.8 - - + +
345i GLY* 1.3 64.4 + - - +
346i GLY 4.0 0.3 + - - -
34k LEU* 4.1 31.2 - - + -
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Residues in contact with GLY 345 (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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341i MET 3.2 19.2 + - - -
342i LYS 4.5 3.8 - - - +
343i ASN 3.6 2.6 - - - +
344i MET* 1.3 81.7 - - - +
346i GLY* 1.3 57.9 + - - -
369i ASP* 3.4 17.1 - - - +
370i ASP* 5.2 4.9 - - - +
373i LEU* 5.4 0.8 - - - +
38k LEU* 4.8 10.8 - - - -
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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