Contacts of the helix formed by residues 350 - 359 (chain A) in PDB entry 3QLE
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 350 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347A ASP* 2.8 34.9 + - - +
349A LYS* 1.3 86.8 - - - +
351A LEU* 1.3 61.8 + - - +
352A ALA 3.3 2.4 + - - -
353A GLU* 3.3 15.5 + - + +
354A GLU* 3.0 29.3 + - + +
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Residues in contact with LEU 351 (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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307A ILE* 4.2 16.2 - - + -
323A LEU* 4.7 10.1 - - + -
326A PHE* 3.4 45.3 - - + -
342A LEU* 3.6 31.2 - - + +
345A PHE* 3.7 33.3 - - + -
347A ASP 3.6 3.8 + - - -
348A LYS* 3.2 20.7 + - + +
349A LYS 3.5 1.4 + - - -
350A ASN* 1.3 77.8 - - - +
352A ALA* 1.3 61.0 + - - +
354A GLU* 3.3 1.4 + - - +
355A PHE* 2.8 33.8 + - + +
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Residues in contact with ALA 352 (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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319A LYS 5.5 0.7 - - - +
322A ARG* 3.3 40.7 - - + +
323A LEU* 4.3 14.9 - - + +
326A PHE* 5.5 2.0 - - + -
350A ASN 3.4 0.6 - - - -
351A LEU* 1.3 85.2 - - - +
353A GLU* 1.3 58.8 + - - +
355A PHE* 3.7 6.3 - - - +
356A ASP* 3.0 28.6 + - - +
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Residues in contact with GLU 353 (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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350A ASN* 3.3 15.6 + - + +
351A LEU 3.3 0.2 - - - -
352A ALA* 1.3 77.3 - - - +
354A GLU* 1.3 66.2 + - + +
356A ASP* 3.2 7.5 + - - +
357A HIS* 3.1 46.7 + - + +
1002A 1PE 4.5 18.4 - - - +
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Residues in contact with GLU 354 (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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345A PHE* 3.5 23.0 - - + +
346A GLU* 2.8 33.3 + - - +
347A ASP* 2.7 41.2 + - - +
350A ASN* 3.0 21.8 + - + +
351A LEU 3.8 0.2 - - - +
353A GLU* 1.3 77.8 - - + +
355A PHE* 1.3 63.6 + - - +
357A HIS* 3.2 9.8 + - - +
358A ARG* 3.0 32.5 + - + +
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Residues in contact with PHE 355 (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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103A ACT 4.2 13.5 - - + -
325A PRO* 3.9 7.2 - - + -
326A PHE* 3.7 44.9 - + + -
329A TYR* 3.6 45.8 - + + -
341A ILE* 6.2 1.1 - - + -
345A PHE* 3.8 17.9 - + + -
351A LEU 2.8 21.7 + - - +
352A ALA* 3.7 7.2 - - - +
354A GLU* 1.3 73.6 - - - +
356A ASP* 1.3 64.6 + - - +
358A ARG* 3.1 14.4 + - + -
359A VAL* 3.1 49.6 + - + +
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Residues in contact with ASP 356 (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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101A CA 2.4 53.2 - - - -
102A CA 2.5 26.2 - - - -
103A ACT 3.0 18.1 - - + +
322A ARG* 4.2 10.4 + - - -
352A ALA 3.0 15.0 + - - +
353A GLU* 3.4 12.3 - - - +
355A PHE* 1.3 76.9 - - - +
357A HIS* 1.3 62.3 + - - +
359A VAL 3.0 5.9 - - - +
1002A 1PE 3.4 30.9 - - - +
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Residues in contact with HIS 357 (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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353A GLU* 3.1 43.7 + - + +
354A GLU* 3.2 9.2 + - - +
356A ASP* 1.3 76.5 - - - +
358A ARG* 1.3 61.9 + - + +
359A VAL 3.6 1.4 + - - +
360A LYS* 5.9 1.6 - - - +
1002A 1PE 3.6 43.1 + - - -
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Residues in contact with ARG 358 (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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341A ILE* 5.8 1.6 - - - +
344A SER* 2.6 52.1 + - - -
345A PHE* 3.4 35.8 - - - +
346A GLU 4.3 1.0 - - - +
354A GLU* 3.0 22.3 + - - +
355A PHE* 3.1 11.4 + - + +
357A HIS* 1.3 78.0 - - + +
359A VAL* 1.3 65.6 + - + +
360A LYS* 4.3 1.4 + - - +
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Residues in contact with VAL 359 (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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101A CA 2.4 31.4 - - - -
103A ACT 3.1 29.1 - - + +
329A TYR* 5.7 5.2 - - + -
355A PHE* 3.1 49.1 + - + +
356A ASP 3.0 1.0 - - - +
357A HIS 3.3 1.1 - - - -
358A ARG* 1.3 88.1 - - + +
360A LYS* 1.3 59.3 + - - +
361A LYS* 4.5 7.6 - - + -
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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