Contacts of the helix formed by residues 748 - 754 (chain D) in PDB entry 3V53
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 ALA 748 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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746D PRO* 4.2 0.8 - - - +
747D THR* 1.3 85.0 - - + +
749D LYS* 1.3 54.7 + - - +
750D PRO* 3.9 11.0 - - + -
751D GLU* 3.2 14.1 + - + +
752D LEU* 2.8 34.7 + - - +
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Residues in contact with LYS 749 (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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747D THR 4.2 1.0 + - - -
748D ALA* 1.3 70.1 - - - +
750D PRO* 1.4 67.7 - - + +
752D LEU* 4.1 8.1 - - - -
753D PHE* 3.0 62.2 + - + -
805D GLN* 2.9 29.9 + - - +
808D LEU* 4.0 5.1 - - - +
820D GLU* 3.8 29.7 + - + +
824D VAL* 4.3 13.9 - - + -
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Residues in contact with PRO 750 (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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748D ALA* 3.4 13.0 - - + -
749D LYS* 1.4 99.2 - - + +
751D GLU* 1.3 63.0 + - + +
753D PHE* 4.0 4.8 - - + +
754D ALA* 3.2 23.7 + - - +
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Residues in contact with GLU 751 (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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746D PRO* 3.5 26.1 - - + +
747D THR 5.4 0.2 - - - +
748D ALA* 3.2 14.6 + - + +
750D PRO* 1.3 80.2 - - + +
752D LEU* 1.3 65.8 + - - +
754D ALA* 3.3 9.2 + - - +
755D TYR* 3.1 18.0 + - - -
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Residues in contact with LEU 752 (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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745D ILE* 3.8 9.6 - - + -
746D PRO* 3.5 26.4 - - + +
747D THR 6.5 0.2 - - - -
748D ALA 2.8 18.4 + - - +
749D LYS* 3.3 7.2 + - - +
751D GLU* 1.3 76.3 - - - +
753D PHE* 1.3 70.1 + - + +
755D TYR* 3.0 21.0 + - - +
824D VAL* 3.7 47.1 - - + +
827D TRP* 3.4 26.8 - - + -
828D ARG* 4.4 5.8 - - + +
831D ILE* 3.4 30.7 - - + -
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Residues in contact with PHE 753 (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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749D LYS* 3.0 50.6 + - + +
750D PRO* 4.0 6.3 - - + +
752D LEU* 1.3 95.2 - - + +
754D ALA* 1.3 58.4 + - - +
755D TYR 3.2 3.3 + - - +
804D PRO* 3.4 39.8 - - + +
805D GLN* 3.0 41.5 - - + -
808D LEU* 3.9 6.5 - - + -
823D ILE* 3.8 25.1 - - + -
824D VAL* 4.3 8.7 - - + -
827D TRP* 4.1 9.5 + + + -
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Residues in contact with ALA 754 (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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750D PRO 3.2 16.8 + - - +
751D GLU* 3.3 12.5 + - - +
752D LEU 3.2 0.6 - - - -
753D PHE* 1.3 77.1 - - - +
755D TYR* 1.3 64.5 + - - +
756D PRO* 3.2 8.0 - - - +
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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