Contacts of the strand formed by residues 625 - 633 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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584B GLU* 4.4 6.3 - - - +
616B TYR* 3.7 33.9 - - + +
621B ILE* 5.4 3.6 - - + -
623B LYS 3.5 3.8 + - - +
624B PRO* 1.3 75.4 - - - +
626B SER* 1.3 62.6 + - - +
627B VAL* 3.6 2.0 + - + +
646B LEU* 3.6 4.0 - - - -
647B TYR* 2.9 37.4 + - + +
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Residues in contact with SER 626 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584B GLU* 3.8 14.4 - - - +
625B ALA* 1.3 70.4 - - - +
627B VAL* 1.3 64.7 + - - +
628B PHE* 5.8 1.6 - - - -
645B PHE 3.7 6.6 + - - -
646B LEU* 3.3 16.7 - - - +
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Residues in contact with VAL 627 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582B PHE* 4.9 2.5 - - + -
583B TYR 4.0 8.3 - - - +
584B GLU* 3.9 22.0 - - + +
592B TRP* 4.6 4.3 - - + -
616B TYR* 3.9 16.6 - - + +
625B ALA 4.3 4.5 - - - +
626B SER* 1.3 82.0 - - - +
628B PHE* 1.3 84.9 + - - +
644B PRO* 3.8 1.4 - - - +
645B PHE* 2.9 45.3 + - + +
647B TYR* 3.5 37.2 - - + -
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Residues in contact with PHE 628 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582B PHE* 3.0 7.9 - - - +
583B TYR* 2.7 80.0 + + + +
584B GLU* 5.2 3.6 - - - -
585B GLU* 5.6 4.5 - - + -
626B SER 5.8 2.0 - - - -
627B VAL* 1.3 86.6 - - - +
629B VAL* 1.3 59.3 + - - +
642B PRO* 4.5 13.5 - - + -
643B LYS 3.7 4.7 - - - +
644B PRO* 4.2 28.5 - - + -
645B PHE* 4.8 1.8 - - - -
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Residues in contact with VAL 629 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550B ILE* 4.9 3.8 - - + +
553B MET* 4.4 26.2 - - + -
568B LEU* 6.1 2.0 - - + -
580B ILE* 3.4 25.8 - - + -
581B ARG 3.2 6.3 - - - +
582B PHE* 3.2 35.2 - - + -
583B TYR* 5.0 0.2 - - - -
611B PHE* 5.7 0.4 - - + -
628B PHE* 1.3 74.1 - - - +
630B GLN* 1.3 65.5 + - - +
642B PRO* 3.9 0.6 - - - -
643B LYS* 2.9 48.2 + - + +
644B PRO 5.0 1.1 - - - +
645B PHE* 4.3 10.8 - - + -
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Residues in contact with GLN 630 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550B ILE* 4.3 5.8 - - - -
580B ILE* 3.5 7.8 - - - +
581B ARG* 3.0 69.0 + - + +
583B TYR* 3.7 19.6 + - + -
629B VAL* 1.3 79.4 - - - +
631B LEU* 1.3 66.8 + - - +
639B THR* 3.2 32.8 + - + +
640B SER* 3.2 30.2 + - - +
642B PRO* 4.1 15.5 - - + +
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Residues in contact with LEU 631 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548B LEU* 4.1 13.9 - - + -
549B LYS 3.4 40.2 - - - +
550B ILE* 3.8 12.8 - - + -
568B LEU* 4.4 21.5 - - + -
570B CYS* 4.1 13.5 - - + -
573B VAL* 4.9 4.0 - - + -
578B ILE* 4.1 23.1 - - + -
579B GLN 3.6 2.0 - - - +
580B ILE* 4.4 17.9 - - + -
609B ILE* 4.7 0.7 - - + -
630B GLN* 1.3 77.0 - - - +
632B ARG* 1.3 61.1 + - - +
639B THR* 2.9 10.0 - - - -
640B SER* 2.5 37.1 + - - +
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Residues in contact with ARG 632 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548B LEU* 4.1 1.3 - - - +
578B ILE* 3.7 4.1 - - - +
579B GLN* 3.0 78.5 + - - +
581B ARG* 4.2 31.6 - - + +
593B GLU* 4.3 8.5 + - - -
595B PHE* 4.0 14.6 - - - -
630B GLN* 4.9 1.6 - - - +
631B LEU* 1.3 76.4 - - - +
633B ARG* 1.3 71.1 + - - +
634B LYS 3.6 0.2 + - - -
637B LEU* 3.8 31.9 - - - +
638B GLU 3.0 19.1 - - - +
639B THR* 3.1 21.5 - - + -
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Residues in contact with ARG 633 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351B ARG* 4.6 2.4 - - - +
543B PRO 3.5 7.1 + - - -
544B ASN* 3.4 24.9 - - - +
545B ALA* 2.8 30.6 + - - +
546B SER 2.6 29.2 + - - -
547B ASN* 4.7 1.2 - - - +
548B LEU* 3.9 25.8 - - + +
574B GLN* 6.6 0.4 - - - -
577B ASP* 3.3 22.9 - - - +
578B ILE* 4.7 2.0 - - + +
579B GLN* 4.3 0.2 - - - -
632B ARG* 1.3 73.1 - - - +
634B LYS* 1.3 60.3 + - - +
635B SER* 4.0 1.1 - - - +
636B ASP* 2.7 49.8 + - - +
637B LEU* 2.9 29.5 + - - +
638B GLU* 3.1 25.7 + - - +
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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