Contacts of the strand formed by residues 625 - 632 (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 625 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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584D GLU* 4.6 8.1 - - - +
616D TYR* 4.3 27.4 - - + +
621D ILE* 5.5 2.9 - - + -
623D LYS 3.6 4.7 + - - +
624D PRO* 1.3 75.1 - - - +
626D SER* 1.3 60.8 + - - +
627D VAL* 4.0 1.8 + - + +
646D LEU* 3.1 5.2 - - - +
647D TYR* 2.9 36.2 + - + +
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Residues in contact with SER 626 (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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584D GLU* 3.3 16.1 - - - +
625D ALA* 1.3 73.6 - - - +
627D VAL* 1.3 63.3 + - - +
644D PRO* 5.9 3.7 - - - +
645D PHE 3.4 10.0 + - - -
646D LEU* 2.9 22.4 - - - +
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Residues in contact with VAL 627 (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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582D PHE* 4.6 3.8 - - + -
583D TYR 3.1 13.0 - - - +
584D GLU* 3.6 28.9 - - + +
592D TRP* 4.4 4.5 - - + -
616D TYR* 4.2 12.6 - - + -
625D ALA 4.0 2.4 + - - +
626D SER* 1.3 80.0 - - - +
628D PHE* 1.3 84.1 + - - +
644D PRO* 3.7 1.9 - - - +
645D PHE* 2.9 41.9 + - + +
647D TYR* 3.9 35.9 - - + -
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Residues in contact with PHE 628 (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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581D ARG 4.3 0.9 - - - -
582D PHE* 3.2 4.2 - - - -
583D TYR* 2.7 77.0 + + + +
584D GLU* 5.1 3.8 - - - -
585D GLU* 5.6 5.4 - - + -
627D VAL* 1.3 88.3 - - - +
629D VAL* 1.3 61.9 + - - +
642D PRO* 3.9 21.3 - - + -
643D LYS 3.8 2.7 - - - -
644D PRO* 4.0 29.6 - - + -
645D PHE* 4.9 0.4 - - - -
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Residues in contact with VAL 629 (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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550D ILE* 3.8 4.1 - - + +
553D MET* 4.4 26.0 - - + -
568D LEU* 5.7 2.5 - - + -
580D ILE* 3.6 27.4 - - + -
581D ARG 3.4 4.7 - - - -
582D PHE* 3.8 26.7 - - + +
611D PHE* 5.4 0.4 - - + -
628D PHE* 1.3 75.9 - - - +
630D GLN* 1.3 66.5 + - - +
642D PRO* 5.0 0.2 - - - -
643D LYS* 2.8 49.7 + - + +
644D PRO 4.6 1.8 - - - +
645D PHE* 4.2 12.3 - - + -
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Residues in contact with GLN 630 (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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550D ILE* 3.7 4.5 - - - -
580D ILE* 3.3 5.9 - - - +
581D ARG* 2.7 69.3 + - + +
583D TYR* 3.5 20.1 - - + -
629D VAL* 1.3 78.7 - - - +
631D LEU* 1.3 65.3 + - - +
639D THR* 3.1 40.0 + - - +
640D SER* 3.5 23.8 + - - +
642D PRO* 4.0 16.5 - - + +
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Residues in contact with LEU 631 (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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548D LEU* 4.7 8.3 - - + -
549D LYS* 3.6 33.9 - - - +
550D ILE* 3.5 22.2 - - + -
568D LEU* 4.3 15.9 - - + -
570D CYS* 4.1 12.6 - - + -
573D VAL* 4.6 6.1 - - + -
578D ILE* 4.2 20.4 - - + -
579D GLN 3.2 9.4 - - - +
580D ILE* 3.9 29.4 - - + -
609D ILE* 4.7 2.0 - - + -
630D GLN* 1.3 81.0 - - - +
632D ARG* 1.3 66.6 + - - +
639D THR* 3.6 5.9 - - - -
640D SER* 3.3 23.6 + - - +
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Residues in contact with ARG 632 (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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548D LEU* 4.3 1.7 - - - +
578D ILE* 3.7 4.2 - - - +
579D GLN* 2.9 70.3 + - - +
581D ARG* 3.0 41.6 - - + +
593D GLU* 4.0 5.5 + - - -
595D PHE* 3.7 15.6 - - - -
630D GLN* 4.9 0.9 - - - +
631D LEU* 1.3 78.7 - - - +
633D ARG* 1.3 71.2 + - - +
634D LYS 3.5 0.2 + - - -
637D LEU* 3.9 26.9 - - - +
638D GLU 3.4 8.3 - - - +
639D THR* 3.2 27.6 - - + -
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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