Contacts of the helix formed by residues 616 - 621 (chain A) in PDB entry 1SIW
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 SER 616 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612A TYR 3.7 0.9 + - - -
613A ASN 3.1 13.0 + - - -
614A HIS 3.0 2.4 - - - -
615A SER* 1.3 80.6 - - - +
617A GLN* 1.3 62.9 + - - +
618A TRP* 3.1 9.1 + - - -
619A ARG* 3.3 40.2 + - - +
620A TYR* 3.6 9.8 - - - -
700A GLU* 4.4 5.4 + - - +
726A PHE* 5.1 0.2 - - - -
730A TYR* 3.7 23.0 - - - -
764A LYS* 3.4 21.3 + - - -
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Residues in contact with GLN 617 (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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611A PHE 4.3 2.7 + - - -
612A TYR* 3.1 22.1 + - + +
615A SER* 2.9 23.9 + - - +
616A SER* 1.3 74.8 - - - +
618A TRP* 1.3 64.5 + - - +
620A TYR* 3.3 9.7 + - - -
722A LYS 3.0 22.6 + - - -
723A GLY* 3.7 15.8 + - - -
726A PHE* 3.6 26.5 - - + -
727A MET* 4.6 3.8 - - - +
1189A ARG* 3.3 35.5 + - + +
1190A ILE* 2.6 44.4 + - - +
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Residues in contact with TRP 618 (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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612A TYR* 3.2 59.4 + - + +
613A ASN* 3.3 24.8 + - - +
616A SER* 3.8 9.3 + - - +
617A GLN* 1.3 75.2 - - - +
619A ARG* 1.3 77.6 + - + +
620A TYR 3.0 11.0 + - - -
621A GLU 3.1 5.2 + - - +
641A HIS* 2.9 32.4 + + + -
643A ILE* 3.5 33.0 - - + -
699A PRO* 4.5 6.5 - - + +
700A GLU* 4.2 17.7 - - - -
743A LEU* 3.8 1.8 - - + +
751A PRO* 3.8 18.8 - - + -
754A VAL* 4.0 23.3 - - + -
755A ASP 4.0 7.9 - - - -
756A TRP* 3.8 30.1 - + - -
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Residues in contact with ARG 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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616A SER* 3.5 33.9 - - - +
617A GLN 3.2 0.8 - - - -
618A TRP* 1.3 101.8 - - + +
620A TYR* 1.3 63.6 + - + +
700A GLU* 3.6 25.8 + - - -
730A TYR* 4.2 14.1 + - - -
742A ASP* 3.2 16.8 + - + +
743A LEU* 2.8 33.0 + - - +
756A TRP* 3.5 35.3 - - + -
757A GLN 3.0 29.3 + - - +
758A ASP 3.2 17.4 + - - -
760A GLY* 3.5 15.2 - - - +
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Residues in contact with TYR 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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616A SER 3.6 15.9 - - - -
617A GLN 3.3 8.4 + - - +
618A TRP 3.0 0.8 - - - -
619A ARG* 1.3 82.1 - - + +
621A GLU* 1.3 67.8 + - - +
622A THR* 3.4 14.4 + - - +
726A PHE* 3.4 30.3 - + + -
729A LYS* 3.1 13.9 + - - -
730A TYR* 2.7 31.4 + + - -
738A ILE* 4.0 16.6 - - + +
740A GLY* 4.0 15.3 - - - -
741A LYS 3.7 18.8 - - - +
742A ASP* 3.7 31.8 + - + +
743A LEU* 3.8 4.3 - - - -
745A GLN* 5.2 1.7 + - - -
746A GLN* 5.8 2.2 + - - +
1189A ARG* 3.7 19.5 + - - +
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Residues in contact with GLU 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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612A TYR* 2.6 29.5 + - - +
617A GLN 3.6 2.0 + - - -
618A TRP 3.1 4.8 + - - +
619A ARG 3.6 0.6 - - - -
620A TYR* 1.3 80.1 - - - +
622A THR* 1.3 72.2 + - - +
623A VAL* 3.0 29.0 + - - +
641A HIS* 3.3 32.7 + - + +
642A LEU* 4.0 4.9 - - + -
743A LEU* 3.6 13.7 - - - +
1189A ARG* 3.1 27.2 + - - +
1190A ILE 3.6 3.5 - - - +
1191A THR* 3.4 23.8 + - - +
1192A PRO* 3.9 0.3 - - - +
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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