Contacts of the strand formed by residues 625 - 633 (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 ALA 625 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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584F GLU* 4.4 5.2 - - - +
616F TYR* 3.5 36.8 - - + +
621F ILE* 5.2 2.7 - - + +
623F LYS 4.4 3.6 - - - +
624F PRO* 1.3 74.7 - - - +
626F SER* 1.3 63.9 + - - +
627F VAL* 3.5 3.5 + - - +
646F LEU* 3.6 3.1 - - - -
647F TYR* 2.8 35.7 + - + +
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Residues in contact with SER 626 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584F GLU* 3.5 16.8 - - - +
625F ALA* 1.3 71.8 - - - +
627F VAL* 1.3 62.6 + - - +
644F PRO* 6.5 1.6 - - - -
645F PHE 3.6 4.0 + - - -
646F LEU* 3.0 24.5 - - - +
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Residues in contact with VAL 627 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582F PHE* 4.7 2.9 - - + -
583F TYR 3.8 9.6 - - - +
584F GLU* 3.9 21.5 - - + +
592F TRP* 4.6 3.8 - - + -
616F TYR* 3.9 16.6 - - + -
625F ALA 3.9 4.0 - - - +
626F SER* 1.3 81.9 - - - +
628F PHE* 1.3 80.2 + - - +
644F PRO* 3.8 2.6 - - - +
645F PHE* 2.9 44.2 + - + +
647F TYR* 3.5 38.1 - - + -
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Residues in contact with PHE 628 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581F ARG 3.8 0.5 - - - +
582F PHE* 3.2 6.1 - - - +
583F TYR* 2.8 77.1 + + + +
584F GLU* 5.1 4.5 - - + -
585F GLU* 5.6 4.3 - - + -
627F VAL* 1.3 88.4 - - - +
629F VAL* 1.3 59.8 + - - +
642F PRO* 4.0 19.7 - - + -
643F LYS 3.9 2.5 - - - -
644F PRO* 4.1 26.9 - - + -
645F PHE* 4.7 0.7 - - - +
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Residues in contact with VAL 629 (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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550F ILE* 5.1 3.5 - - + +
553F MET* 4.3 29.2 - - + -
568F LEU* 5.9 3.1 - - + -
580F ILE* 3.6 20.6 - - + -
581F ARG 3.3 6.3 - - - +
582F PHE* 3.5 37.0 - - + -
611F PHE* 5.4 0.2 - - + -
628F PHE* 1.3 75.3 - - - +
630F GLN* 1.3 65.7 + - - +
643F LYS* 2.9 50.6 + - + +
644F PRO 4.7 1.3 - - - +
645F PHE* 4.4 10.1 - - + +
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Residues in contact with GLN 630 (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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550F ILE* 4.6 5.2 - - - -
580F ILE* 3.5 8.5 - - - +
581F ARG* 2.9 73.8 + - + +
583F TYR* 3.6 25.3 + - + -
629F VAL* 1.3 78.5 - - - +
631F LEU* 1.3 68.3 + - - +
639F THR* 3.3 39.3 + - + +
640F SER* 3.3 20.7 + - - +
642F PRO* 4.4 9.6 - - + +
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Residues in contact with LEU 631 (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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548F LEU* 4.1 19.1 - - + -
549F LYS 3.5 40.6 - - - +
550F ILE* 3.8 12.1 - - + +
568F LEU* 4.5 21.8 - - + -
570F CYS* 4.0 12.8 - - + -
573F VAL* 5.0 1.6 - - + -
578F ILE* 4.3 19.3 - - + -
579F GLN 3.6 5.4 - - - +
580F ILE* 4.6 9.9 - - + -
609F ILE* 5.0 1.1 - - + -
630F GLN* 1.3 79.4 - - - +
632F ARG* 1.3 54.0 + - - +
639F THR* 2.8 16.1 - - - -
640F SER* 2.6 44.4 + - - +
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Residues in contact with ARG 632 (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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548F LEU* 4.2 2.2 - - - +
578F ILE* 3.8 4.5 - - - +
579F GLN* 3.0 71.3 + - - +
581F ARG* 4.0 31.6 - - + +
593F GLU* 4.3 5.9 + - - -
595F PHE* 4.0 14.6 - - - -
630F GLN* 4.6 4.7 - - - +
631F LEU* 1.3 75.1 - - - +
633F ARG* 1.3 64.0 + - - +
637F LEU* 3.3 38.7 - - - +
638F GLU 2.8 19.5 - - - +
639F THR* 3.1 20.0 - - + -
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Residues in contact with ARG 633 (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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351F ARG* 4.5 2.0 - - - +
543F PRO 3.3 16.5 + - - -
544F ASN* 3.9 13.8 + - - +
545F ALA* 2.6 32.7 + - - +
546F SER 2.6 29.6 + - - -
547F ASN* 4.6 1.4 - - - +
548F LEU* 3.9 23.0 - - + +
577F ASP* 3.3 26.2 - - - +
578F ILE* 5.4 0.9 - - + -
632F ARG* 1.3 74.1 - - - +
634F LYS* 1.3 60.8 + - - +
635F SER* 3.9 0.9 - - - +
636F ASP* 2.7 53.3 + - - +
637F LEU* 2.9 28.9 - - - +
638F GLU* 3.1 22.5 + - - +
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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