Contacts of the strand formed by residues 613 - 616 (chain C) in PDB entry 3QCA
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 TYR 613 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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581C PRO* 3.9 18.7 - - + +
607C GLY 4.9 0.7 - - - -
608C PHE* 4.1 26.9 - + - -
609C PRO* 2.9 25.7 + - + +
610C TRP* 3.1 30.9 - - - +
611C ASP 3.5 1.4 - - - -
612C GLU* 1.3 95.6 - - + +
614C LYS* 1.3 61.5 + - - +
625C THR* 3.6 2.3 + - - +
646C LEU* 3.6 26.7 - - + +
647C GLU 3.2 25.8 - - - +
648C ALA* 3.5 20.7 - - + +
649C LYS* 4.7 1.1 - - - +
628D ASP* 2.9 37.4 + - - +
631D LYS* 3.8 16.7 - - + +
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Residues in contact with LYS 614 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613C TYR* 1.3 73.0 - - - +
615C LEU* 1.3 59.5 + - - +
616C LEU* 3.5 22.4 + - + +
623C ASP* 4.4 10.8 - - + -
625C THR* 4.1 7.2 - - - +
645C PHE 3.0 14.2 - - - +
646C LEU* 3.3 2.7 - - - -
647C GLU* 2.8 31.9 + - + +
648C ALA 5.9 0.2 - - - -
649C LYS* 5.1 10.2 - - + +
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Residues in contact with LEU 615 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578C ILE* 3.5 18.4 - - + -
599C VAL* 4.3 20.0 - - + -
600C PHE* 5.2 5.6 - - + -
603C VAL* 4.6 17.5 - - + -
614C LYS* 1.3 69.9 - - - +
616C LEU* 1.3 59.3 + - - +
623C ASP* 4.7 0.2 - - - +
624C VAL* 2.7 48.3 + - + +
625C THR* 3.5 24.6 + - + +
644C LEU* 3.4 43.7 - - + -
645C PHE 3.7 8.1 - - - +
646C LEU* 4.1 14.6 - - + -
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Residues in contact with LEU 616 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614C LYS* 3.5 31.6 - - + +
615C LEU* 1.3 73.7 - - - +
617C SER* 1.3 65.7 + - - +
618C THR 3.8 0.2 + - - -
621C ARG* 4.2 25.4 - - + +
622C ARG 3.2 2.2 - - - +
623C ASP* 3.8 16.6 - - + +
644C LEU* 3.3 9.4 - - - -
645C PHE* 2.7 47.5 + - + +
647C GLU* 5.0 17.0 - - - +
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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