Contacts of the helix formed by residues 619 - 624 (chain A) in PDB entry 3W3K
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 ARG 619 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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595A ASN* 4.0 29.1 + - - +
596A ILE 3.1 13.3 + - - +
597A TYR* 3.8 12.1 - - + -
618A ASN* 1.3 83.4 - - - +
620A LEU* 1.3 62.5 + - - +
621A ASP* 2.8 40.0 + - - +
622A ILE* 3.6 27.4 - - + +
623A LEU* 3.2 26.9 + - - +
649A ASN* 3.8 0.4 - - - -
650A ARG* 2.9 45.0 - - - +
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Residues in contact with LEU 620 (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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615A PHE* 3.8 19.3 - - + -
619A ARG* 1.3 72.0 - - - +
621A ASP* 1.3 58.8 + - - +
622A ILE 3.2 0.7 - - - -
623A LEU* 3.9 20.0 - - + -
624A TRP* 2.7 76.0 + - + +
634A ILE* 4.7 2.7 - - + -
635A PHE* 4.0 7.2 - - + -
646A LEU* 3.7 33.4 - - + -
649A ASN* 3.0 41.9 + - + +
651A LEU* 3.7 13.7 - - + -
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Residues in contact with ASP 621 (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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619A ARG* 2.8 48.3 + - - +
620A LEU* 1.3 79.5 - - - +
622A ILE* 1.3 65.6 + - - +
624A TRP* 4.1 1.1 - - - -
625A ASN* 3.4 20.6 + - - +
649A ASN 3.4 10.1 + - - +
650A ARG* 3.3 29.6 - - - +
651A LEU* 3.5 14.9 - - + +
652A LYS 5.3 0.7 - - - +
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Residues in contact with ILE 622 (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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597A TYR* 3.8 43.5 - - + +
619A ARG* 3.5 38.1 + - + +
620A LEU 3.2 0.4 - - - -
621A ASP* 1.3 88.4 + - - +
623A LEU* 1.3 65.5 + - - +
624A TRP 3.2 0.4 - - - -
625A ASN* 3.2 19.8 + - - +
628A ASP* 4.8 5.0 - - - +
460B GLU* 3.4 39.0 - - + +
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Residues in contact with LEU 623 (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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596A ILE* 3.4 20.4 - - + +
597A TYR* 3.3 28.3 - - - +
598A THR* 4.1 1.1 - - - +
599A LEU* 5.5 0.7 - - + -
615A PHE* 4.0 16.2 - - + -
619A ARG 3.2 20.0 + - - +
620A LEU* 3.3 28.2 + - + +
622A ILE* 1.3 79.7 - - - +
624A TRP* 1.3 60.8 + - + +
625A ASN 3.4 0.7 + - - -
628A ASP* 4.3 9.7 - - - +
631A TYR* 3.3 65.4 + - + +
634A ILE* 4.4 6.5 - - + -
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Residues in contact with TRP 624 (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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620A LEU* 2.7 47.0 + - + +
621A ASP* 4.1 2.5 - - - -
623A LEU* 1.3 75.1 - - + +
625A ASN* 1.3 67.2 + - - +
626A ASP* 3.3 2.4 + - - -
628A ASP 4.7 3.3 - - - +
631A TYR* 3.0 36.8 + - + -
632A ILE* 4.0 6.8 - - + +
634A ILE* 3.8 7.9 - - + +
635A PHE* 3.9 33.2 - + - -
646A LEU* 4.1 18.6 - - + -
651A LEU* 4.2 11.7 - - + -
653A HIS* 5.9 0.7 - - - -
654A ILE* 3.6 34.5 - - + -
655A PRO* 3.5 28.3 - - + +
658A ALA* 4.0 30.9 - - + +
662A LEU* 4.4 8.5 - - + -
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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