Contacts of the strand formed by residues 608 - 612 (chain D) 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 ALA 608 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215C LEU* 4.2 18.6 - - + -
248C VAL* 6.2 0.2 - - + -
249C ALA* 5.2 0.7 - - + -
567D TYR* 6.5 0.2 - - + -
568D LEU 3.2 14.1 - - - +
569D LEU* 3.5 20.6 - - + -
570D CYS* 3.9 2.0 - - - -
603D VAL* 3.3 3.8 - - - +
604D HIS* 3.0 38.2 + - + +
606D GLN 3.8 0.8 - - - -
607D PHE* 1.3 81.6 - - + +
609D ILE* 1.3 72.7 + - - +
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Residues in contact with ILE 609 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566D ILE 3.4 4.3 - - - +
568D LEU* 2.8 37.0 + - + +
570D CYS* 4.7 7.6 - - - -
573D VAL* 4.8 4.3 - - + -
578D ILE* 3.8 24.9 - - + -
580D ILE* 3.8 28.9 - - + -
598D PHE* 3.5 36.3 - - + -
602D ASP 3.7 3.1 - - - +
603D VAL* 3.9 21.3 - - + -
608D ALA* 1.3 84.4 - - - +
610D VAL* 1.3 67.4 + - - +
611D PHE* 3.6 9.4 + - + -
631D LEU* 4.7 5.6 - - + -
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Residues in contact with VAL 610 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C ARG* 3.9 28.3 - - - +
215C LEU* 4.0 27.1 - - + -
565D GLU* 3.5 28.7 - - + +
566D ILE 3.4 3.6 - - - +
567D TYR* 3.4 36.1 - - + -
598D PHE* 3.4 3.6 - - - +
602D ASP* 3.2 38.6 + - - +
604D HIS* 5.8 0.2 - - + -
609D ILE* 1.3 75.0 - - - +
611D PHE* 1.3 58.7 + - - +
612D LYS* 4.9 0.8 + - - -
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Residues in contact with PHE 611 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553D MET* 4.7 8.7 - - + -
565D GLU* 3.3 7.0 - - - +
566D ILE* 2.8 73.0 + - + -
568D LEU* 4.1 17.9 - - + -
580D ILE* 4.2 12.8 - - + -
582D PHE* 3.5 36.8 - + - -
596D GLY* 3.7 17.0 - - - -
597D ASP 3.2 14.1 - - - +
598D PHE* 3.6 18.2 - - + -
609D ILE* 3.8 14.4 - - + -
610D VAL* 1.3 74.4 - - - +
612D LYS* 1.3 75.1 + - - +
613D THR* 4.2 10.1 - - - -
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Residues in contact with LYS 612 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563D GLY* 3.3 26.7 - - - +
564D GLU 3.1 4.3 - - - +
565D GLU* 4.3 16.9 + - + -
595D PHE 4.3 0.3 - - - +
596D GLY* 3.7 1.4 - - - -
597D ASP* 2.8 73.4 + - + +
598D PHE* 4.6 1.6 - - - +
602D ASP* 4.3 15.0 + - - -
610D VAL 4.9 0.4 + - - -
611D PHE* 1.3 82.7 - - - +
613D THR* 1.3 67.9 + - - +
614D PRO* 3.5 0.7 - - - +
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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