Contacts of the helix formed by residues 788 - 793 (chain A) in PDB entry 1Q2L
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 TYR 788 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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784A GLN* 3.0 28.0 + - - +
785A PRO* 3.3 17.7 - - + +
786A TRP 3.1 0.4 - - - -
787A PHE* 1.3 74.3 - - - +
789A ASN* 1.3 53.5 + - - +
790A GLN 3.0 3.3 + - - -
791A LEU* 3.2 42.1 + - + +
792A ARG* 3.0 48.7 + - + +
799A TYR* 3.1 44.4 + + - -
801A VAL* 4.4 14.8 - - - -
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Residues in contact with ASN 789 (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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786A TRP 2.9 18.6 + - - +
787A PHE 2.6 4.9 + - - -
788A TYR* 1.3 72.5 - - - +
790A GLN* 1.3 68.4 + - - +
791A LEU 3.2 0.4 - - - -
792A ARG* 3.8 24.5 - - - +
793A THR* 3.0 40.4 + - - +
794A GLU* 3.3 12.2 + - - +
835A PHE* 4.1 20.6 - - - -
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Residues in contact with GLN 790 (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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787A PHE* 2.7 44.9 + - + +
789A ASN* 1.3 88.9 - - - +
791A LEU* 1.3 56.3 + - - +
794A GLU* 2.9 42.9 + - - +
795A GLU 3.1 2.9 + - - -
796A GLN* 3.2 20.4 + - - +
801A VAL* 3.7 7.0 - - + -
818A LEU* 3.5 28.8 - - + +
831A ARG* 3.8 22.0 + - - +
832A TYR* 3.6 19.9 - - - -
835A PHE* 4.8 5.1 - - + +
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Residues in contact with LEU 791 (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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788A TYR* 3.2 57.6 + - + +
790A GLN* 1.3 80.4 - - - +
792A ARG* 1.3 69.0 + - + +
795A GLU* 3.0 31.0 - - - +
796A GLN 4.0 0.9 - - - +
797A LEU 3.0 26.5 - - - +
798A GLY* 5.7 0.2 - - - -
799A TYR* 3.7 18.2 - - + +
801A VAL* 3.5 25.4 - - + -
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Residues in contact with ARG 792 (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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785A PRO* 2.9 33.2 + - - +
786A TRP* 4.0 3.8 + - - +
788A TYR* 3.0 41.7 + - + +
789A ASN* 3.8 22.9 - - - +
791A LEU* 1.3 85.2 - - + +
793A THR* 1.3 62.8 + - - +
795A GLU* 3.7 8.3 - - - +
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Residues in contact with THR 793 (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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789A ASN* 3.0 28.1 + - - +
792A ARG* 1.3 81.0 + - - +
794A GLU* 1.3 78.6 + - - +
795A GLU* 3.2 12.0 + - - +
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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