Contacts of the strand formed by residues 643 - 648 (chain F) in PDB entry 3GUT
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 LYS 643 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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549F LYS* 6.0 2.2 - - - +
550F ILE* 3.8 37.2 + - + -
551F VAL 5.0 4.6 + - - +
553F MET* 4.4 21.5 - - + -
556F THR* 5.6 5.4 - - + -
628F PHE* 4.2 2.9 - - - -
629F VAL* 2.9 47.5 + - + +
641F GLU* 3.0 14.7 + - - +
642F PRO* 1.3 76.2 + - - +
644F PRO* 1.4 77.6 - - + +
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Residues in contact with PRO 644 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553F MET* 5.7 0.5 - - - +
556F THR* 3.9 18.1 - - - +
626F SER* 6.5 1.1 - - - -
627F VAL 3.8 9.6 - - - +
628F PHE* 4.1 14.5 - - + -
629F VAL* 4.7 1.9 - - - +
642F PRO 4.1 4.3 - - - +
643F LYS* 1.4 99.2 - - + +
645F PHE* 1.3 58.8 + - - +
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Residues in contact with PHE 645 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553F MET* 4.6 9.6 - - + -
555F ARG 4.0 9.9 - - - -
556F THR* 3.1 29.8 - - - -
557F ALA 3.6 4.0 - - - -
558F GLY* 3.5 30.1 - - - -
566F ILE* 5.2 4.7 - - + -
582F PHE* 3.7 28.7 - + + -
611F PHE* 6.2 0.4 - + - -
613F THR* 3.9 19.1 - - - -
626F SER* 3.6 4.4 - - - -
627F VAL* 2.9 55.8 + - + +
629F VAL* 4.4 10.3 - - + -
643F LYS 4.5 0.2 - - - +
644F PRO* 1.3 74.5 - - - +
646F LEU* 1.3 63.7 + - - +
647F TYR* 3.7 27.1 - + - -
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Residues in contact with LEU 646 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556F THR 2.7 11.0 + - - +
557F ALA* 3.0 14.4 - - + +
558F GLY 2.8 30.1 + - - +
624F PRO* 3.4 22.0 - - + -
625F ALA 3.6 6.3 - - - +
626F SER* 3.0 41.1 - - - +
645F PHE* 1.3 76.9 - - - +
647F TYR* 1.3 71.6 + - - +
648F TYR* 3.5 12.7 + - + +
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Residues in contact with TYR 647 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558F GLY 3.1 8.3 - - - -
559F CYS 2.9 31.6 - - - -
560F VAL* 3.8 22.0 - - + +
582F PHE* 4.3 4.5 - + - -
592F TRP* 4.0 13.9 - + - -
613F THR* 3.2 16.2 - - + +
614F PRO* 2.7 43.8 + - - +
616F TYR* 3.7 29.2 - + + -
621F ILE* 4.8 0.5 - - - +
624F PRO* 3.2 1.7 - - - +
625F ALA* 2.8 38.7 + - + +
627F VAL* 3.5 29.8 - - + -
645F PHE* 3.7 14.5 + + - -
646F LEU* 1.3 71.9 - - - +
648F TYR* 1.3 61.4 + - - +
649F PRO 4.2 0.2 - - - -
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Residues in contact with TYR 648 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555F ARG* 3.1 31.9 + - - -
557F ALA* 4.0 5.6 - - + -
558F GLY 3.1 14.8 + - - -
559F CYS* 3.2 36.8 + - + -
560F VAL* 3.2 5.4 + - - -
564F GLU* 3.4 17.0 + - - -
624F PRO* 3.8 7.9 - - + -
646F LEU* 3.9 19.5 - - + -
647F TYR* 1.3 73.3 - - - +
649F PRO* 1.3 79.8 - - + +
650F GLU* 5.9 1.3 - - + -
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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