Contacts of the strand formed by residues 616 - 619 (chain E) in PDB entry 6IWQ
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 616 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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609E GLN 3.8 0.9 - - - +
610E TYR* 3.6 3.5 - - - -
611E PHE* 2.9 40.2 + - + +
614E LEU* 2.7 47.3 - - + +
615E HIS* 1.3 79.2 - - - +
617E PHE* 1.3 74.5 + - - +
618E THR* 3.5 21.3 - - + +
625E CYS* 3.7 12.9 - - + -
640E CYS* 3.4 29.6 - - - -
642E SER* 4.2 16.8 + - - -
647E GLN 4.3 9.1 + - - +
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Residues in contact with PHE 617 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537E ILE* 3.6 31.2 - - + -
573E ILE* 3.5 30.1 - - + -
579E LEU* 4.4 20.9 - - + -
608E TRP* 5.1 9.0 - - + -
609E GLN 3.6 4.3 - - - -
610E TYR* 3.6 36.3 - + + -
615E HIS 4.2 0.4 + - - -
616E ARG* 1.3 76.6 - - - +
618E THR* 1.3 60.1 + - - +
625E CYS* 3.4 4.5 - - - +
626E LEU* 3.0 49.6 + - + +
647E GLN 5.1 0.7 + - - +
649E TRP* 4.0 24.6 - + + -
650E GLU 5.0 0.7 - - - -
651E MET* 4.1 17.3 - - + -
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Residues in contact with THR 618 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608E TRP* 3.7 7.0 - - - -
609E GLN* 3.0 48.7 + - + +
611E PHE* 3.6 21.3 - - + -
616E ARG* 3.5 27.6 - - + +
617E PHE* 1.3 77.1 - - - +
619E HIS* 1.3 70.5 + - - +
620E ILE* 3.6 3.1 + - - +
623E GLY* 4.7 3.9 + - - -
624E LYS 3.6 9.2 + - - -
625E CYS* 4.1 5.6 - - - -
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Residues in contact with HIS 619 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588E LYS* 3.3 42.4 - - + +
607E GLU* 3.2 32.8 + - + -
608E TRP* 4.1 29.2 - + + -
618E THR* 1.3 78.6 + - - +
620E ILE* 1.3 56.2 + - - +
621E PRO* 3.3 23.7 - - + +
622E SER* 2.5 51.3 + - - +
623E GLY* 4.1 1.4 - - - -
624E LYS 2.8 19.8 + - - +
625E CYS* 4.5 1.0 - - - +
626E LEU 5.0 0.2 - - - +
637E ILE* 3.8 12.5 - - + +
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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
------------------------------------------------------------
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