Contacts of the helix formed by residues 618 - 623 (chain A) in PDB entry 3S1Q
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 GLU 618 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528A LEU* 3.9 13.2 - - - -
531A ILE* 4.5 0.4 - - - -
532A ARG* 4.4 8.5 - - + -
590A ARG* 3.9 3.5 + - - -
616A VAL* 3.5 12.6 + - + +
617A VAL* 1.3 75.3 - - - +
619A LYS* 1.4 75.2 + - - +
620A LYS* 3.0 54.6 + - - +
621A THR* 2.9 20.0 + - - -
622A VAL* 3.1 11.7 + - - +
748A MET 4.3 12.4 - - - +
749A ALA* 3.5 24.7 - - - +
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Residues in contact with LYS 619 (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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528A LEU* 3.5 19.8 - - + +
618A GLU* 1.4 77.0 - - - +
620A LYS* 1.3 57.5 + - - +
623A GLY* 2.6 39.7 + - - +
624A SER* 5.4 4.9 - - - +
625A SER* 3.1 7.9 + - - +
749A ALA 3.2 16.0 + - - +
750A GLY* 3.4 26.0 + - - +
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Residues in contact with LYS 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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590A ARG* 3.6 23.7 + - - +
592A ASP* 3.5 35.8 - - - +
618A GLU* 3.0 35.4 + - - +
619A LYS* 1.3 74.0 - - + +
621A THR* 1.3 56.4 + - - +
625A SER* 3.1 24.6 + - - -
627A GLY 4.9 1.7 - - - +
628A GLY* 4.2 4.5 + - - -
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Residues in contact with THR 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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588A LEU* 4.6 7.0 - - + -
590A ARG* 3.3 24.4 + - - +
605A MET* 3.8 31.7 - - + -
607A ILE* 4.7 5.4 - - + -
616A VAL 4.1 1.4 + - - -
617A VAL* 3.9 20.7 - - + -
618A GLU* 2.9 17.5 + - - -
620A LYS* 1.3 77.5 - - - +
622A VAL* 1.3 58.1 + - - -
623A GLY 3.6 1.2 - - - +
628A GLY* 3.4 6.1 - - - -
629A LEU* 2.8 44.2 + - + +
630A ILE 4.5 0.2 + - - -
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Residues in contact with VAL 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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523A ILE* 2.9 67.8 + - + -
528A LEU* 3.7 11.9 - - + -
531A ILE* 4.0 12.1 - - + -
617A VAL* 3.8 20.2 - - + -
618A GLU 3.1 14.1 + - - +
621A THR* 1.3 76.5 - - + +
623A GLY* 1.3 60.7 + - - +
629A LEU* 4.9 8.5 - - + -
630A ILE* 3.4 14.3 - - + +
649A ILE* 4.2 15.7 - - + -
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Residues in contact with GLY 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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519A PRO* 5.6 0.3 - - - +
522A GLY* 4.2 8.5 - - - -
523A ILE 4.5 6.3 - - - -
619A LYS* 2.6 37.7 + - - -
621A THR 3.6 2.7 - - - +
622A VAL* 1.3 77.8 - - - +
624A SER* 1.4 57.5 + - - -
625A SER* 3.0 16.5 + - - +
628A GLY* 5.1 1.6 - - - -
630A ILE* 3.4 15.1 - - - +
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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