Contacts of the helix formed by residues 42 - 46 (chain D) in PDB entry 2QLR
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 42 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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325C PHE* 3.6 14.6 - - + -
326C TYR* 3.0 16.6 + - + +
403C SER* 3.0 30.6 + - - +
404C SER* 3.8 9.7 - - - -
428C GOL 3.1 26.9 + - - -
41D PRO* 1.3 68.9 - - - +
43D PRO* 1.3 63.9 - - - +
44D ASN* 2.9 61.1 + - - +
45D MET* 3.2 22.1 + - + +
46D PHE* 4.1 7.1 - - - -
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Residues in contact with PRO 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404C SER* 5.3 2.0 - - - +
41D PRO 3.1 10.4 - - - +
42D ASN* 1.3 86.1 - - - +
44D ASN* 1.3 61.4 + - - +
45D MET 3.1 2.0 - - - -
46D PHE* 3.3 39.7 + - + +
49D LYS* 4.8 1.0 + - - -
69D LYS* 4.0 47.5 - - + +
72D LEU* 5.4 0.9 - - - +
73D GLN* 3.4 20.0 - - + +
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Residues in contact with ASN 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C GLU* 5.1 2.9 - - - +
325C PHE* 6.3 0.4 - - + -
428C GOL 4.1 13.7 + - - -
42D ASN* 2.9 28.9 - - - +
43D PRO* 1.3 71.6 - - - +
45D MET* 1.3 74.3 + - + +
46D PHE 3.2 1.1 - - - -
49D LYS* 3.0 24.5 + - - +
65D GLU* 5.4 0.3 - - - +
69D LYS* 3.3 34.6 + - - +
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Residues in contact with MET 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C GLU* 5.8 0.8 - - - +
263C LLP 4.6 7.2 - - - +
264C ILE 4.0 1.0 - - - +
318C HIS* 3.3 21.8 + - - -
321C ARG 4.9 1.3 - - - +
322C VAL* 3.6 32.2 - - + +
325C PHE* 3.6 46.2 - - + -
326C TYR* 3.8 24.5 - - + -
42D ASN* 3.2 18.1 + - + +
43D PRO 3.1 0.6 - - - -
44D ASN* 1.3 94.4 - - + +
46D PHE* 1.3 67.5 + - + +
47D PRO* 3.6 0.3 - - - +
49D LYS* 4.7 0.2 - - - -
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Residues in contact with PHE 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C GLU* 5.4 0.2 - - - +
262C SER 3.1 28.7 - - - -
263C LLP 3.5 20.0 - - - -
264C ILE 3.8 6.3 - - - -
265C ILE 3.2 24.9 - - - +
266C SER* 3.8 6.3 - - - -
267C SER* 3.7 12.3 - - - -
41D PRO* 4.1 9.2 - - + -
42D ASN 4.1 7.9 - - - -
43D PRO* 3.3 33.7 + - + +
44D ASN 3.2 1.8 - - - -
45D MET* 1.3 81.9 - - + +
47D PRO* 1.4 60.1 - - - +
48D PHE 3.5 3.4 + - - +
49D LYS* 2.8 29.1 + - - -
72D LEU* 3.4 48.9 - - + -
73D GLN* 4.7 1.6 - - - -
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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