Contacts of the helix formed by residues 643 - 647 (chain A) in PDB entry 2PDA
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 VAL 643 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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638A PHE* 3.3 36.7 + - + -
639A PHE* 3.2 46.0 - - + -
642A VAL* 1.3 75.4 - - - +
644A LYS* 1.3 60.3 + - - +
647A LEU* 2.8 41.5 + - + +
669A THR* 4.0 20.6 - - + +
673A GLU* 5.4 1.1 - - - +
849A PRO* 3.7 23.1 - - + +
850A SER 5.4 0.4 - - - +
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Residues in contact with LYS 644 (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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632A GLU* 5.6 8.1 - - - +
633A PRO* 6.0 2.6 - - - +
635A THR* 5.7 3.6 - - + -
639A PHE* 2.8 44.1 + - + +
640A LYS* 4.3 7.6 - - - +
643A VAL* 1.3 71.5 - - - +
645A PRO* 1.3 75.1 - - + +
647A LEU* 3.1 6.8 + - + -
648A THR* 2.9 44.0 + - + +
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Residues in contact with PRO 645 (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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640A LYS 3.5 18.6 - - - +
641A ASN 3.8 13.5 - - - +
642A VAL 3.2 14.6 - - - +
644A LYS* 1.3 95.9 - - + +
646A ILE* 1.3 57.3 + - - +
648A THR* 3.3 11.0 + - - +
650A GLN* 2.8 46.9 + - + +
654A LEU* 4.2 12.3 - - + -
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Residues in contact with ILE 646 (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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642A VAL* 3.2 33.5 + - + +
643A VAL 4.1 0.2 - - - +
644A LYS 3.2 0.4 - - - -
645A PRO* 1.3 74.9 - - - +
647A LEU* 1.3 61.2 + - - +
649A GLN* 2.9 25.1 + - - -
651A GLY* 4.0 12.3 - - - +
654A LEU* 3.6 19.3 - - + -
659A PHE* 5.0 0.4 - - + -
665A PHE* 5.2 1.8 - - + -
848A ALA 5.3 0.2 - - - +
849A PRO* 3.5 42.2 - - + -
223B ASP* 3.6 24.9 - - - +
224B ILE* 4.1 23.3 - - + -
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Residues in contact with LEU 647 (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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458A LYS* 5.5 4.3 - - - +
498A TYR* 3.4 23.7 + - - -
639A PHE* 4.2 8.5 - - + -
643A VAL* 2.8 39.9 - - + +
644A LYS* 3.1 7.1 + - + +
646A ILE* 1.3 76.6 - - + +
648A THR* 1.3 61.3 + - + +
649A GLN* 3.2 6.6 + - - +
673A GLU* 3.7 38.1 - - + +
849A PRO* 3.4 25.8 - - + -
850A SER* 4.8 2.0 - - - -
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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