Contacts of the strand formed by residues 625 - 631 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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584H GLU* 4.7 6.5 - - - +
616H TYR* 4.3 28.7 - - + +
621H ILE* 5.3 3.3 - - + +
623H LYS 3.6 4.2 + - - +
624H PRO* 1.3 74.5 - - - +
626H SER* 1.3 60.5 + - - +
627H VAL* 4.0 1.9 + - + +
646H LEU* 2.9 4.9 - - - +
647H TYR* 2.7 40.8 + - + +
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Residues in contact with SER 626 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584H GLU* 3.5 15.2 - - - +
625H ALA* 1.3 72.0 - - - +
627H VAL* 1.3 63.5 + - - +
644H PRO* 6.0 3.7 - - - +
645H PHE 3.4 9.3 + - - -
646H LEU* 2.8 23.3 - - - +
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Residues in contact with VAL 627 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582H PHE* 4.6 4.0 - - + -
583H TYR 3.1 14.8 - - - +
584H GLU* 3.6 29.6 - - + +
592H TRP* 4.5 2.9 - - + -
616H TYR* 4.1 19.7 - - + -
625H ALA 4.0 2.7 + - - +
626H SER* 1.3 78.5 - - - +
628H PHE* 1.3 90.7 + - - +
644H PRO* 3.8 2.8 - - - +
645H PHE* 3.1 34.0 + - + +
647H TYR* 4.0 28.5 - - + -
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Residues in contact with PHE 628 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581H ARG 4.4 0.7 - - - -
582H PHE* 3.1 6.6 - - - +
583H TYR* 2.7 75.2 + + + +
584H GLU* 5.1 3.6 - - - -
585H GLU* 5.5 5.4 - - + -
626H SER 6.1 0.2 - - - -
627H VAL* 1.3 92.8 - - - +
629H VAL* 1.3 61.2 + - - +
642H PRO* 4.0 17.9 - - + -
643H LYS 3.5 17.9 - - - +
644H PRO* 4.1 17.9 - - + -
645H PHE* 4.7 1.1 - - - +
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Residues in contact with VAL 629 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550H ILE* 3.9 4.5 - - + +
553H MET* 4.6 24.9 - - + -
568H LEU* 5.6 3.1 - - + -
580H ILE* 3.5 28.7 - - + -
581H ARG 3.4 5.6 - - - +
582H PHE* 4.0 23.1 - - + -
611H PHE* 5.3 0.7 - - + -
628H PHE* 1.3 77.2 - - - +
630H GLN* 1.3 65.9 + - - +
631H LEU* 6.4 0.2 - - + -
642H PRO* 5.0 0.2 - - - -
643H LYS* 2.9 44.9 + - + +
644H PRO 4.7 1.8 - - - +
645H PHE* 4.2 12.3 - - + -
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Residues in contact with GLN 630 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550H ILE* 3.9 3.6 - - - -
580H ILE* 3.5 1.6 - - - -
581H ARG* 2.7 71.2 + - + +
583H TYR* 3.6 18.4 - - + -
629H VAL* 1.3 80.6 - - - +
631H LEU* 1.3 65.6 + - - +
639H THR* 3.1 40.9 + - - +
640H SER* 3.3 23.6 + - - +
641H GLU 4.5 3.4 - - - +
642H PRO* 4.2 12.6 - - + +
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Residues in contact with LEU 631 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548H LEU* 4.5 8.3 - - + -
549H LYS 4.0 31.2 - - - +
550H ILE* 3.8 11.7 - - + -
568H LEU* 4.3 20.2 - - + -
570H CYS* 4.0 15.5 - - + -
573H VAL* 4.5 6.5 - - + -
578H ILE* 4.1 23.3 - - + -
579H GLN 3.1 9.4 - - - +
580H ILE* 3.7 31.6 - - + -
609H ILE* 4.6 1.1 - - + -
629H VAL* 6.4 0.4 - - + -
630H GLN* 1.3 85.3 - - - +
632H ARG* 1.3 66.3 + - - +
639H THR* 3.5 10.2 - - - -
640H SER* 3.4 13.4 + - - +
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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