Contacts of the strand formed by residues 617 - 623 (chain B) in PDB entry 6AHU
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 GLY 617 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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433B ARG* 4.8 3.4 - - - -
434B LEU 3.3 7.0 - - - -
435B ILE* 3.7 17.5 - - - -
600B ILE 3.9 0.2 - - - +
601B GLN* 3.3 3.1 + - - +
602B GLN* 2.6 50.4 + - - +
615B GLY 3.6 2.0 + - - -
616B SER* 1.3 74.0 - - - +
618B TRP* 1.3 63.1 + - - -
619B ASP* 4.4 1.8 - - - +
650B HIS* 5.9 1.3 - - - -
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Residues in contact with TRP 618 (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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433B ARG* 3.3 0.5 - - - -
434B LEU* 2.5 53.4 + - + +
439B SER* 4.6 11.9 - - - -
440B HIS* 3.1 41.7 + + - -
443B LEU* 3.8 31.6 - - + -
490B LEU* 4.8 14.6 - - + -
496B PRO* 3.4 27.1 - - + +
499B ILE* 5.2 7.2 - - + -
503B THR* 4.7 10.8 - - + -
505B LEU* 6.0 2.9 - - + -
599B LEU* 4.1 27.1 - - + -
600B ILE 3.2 13.0 - - - -
601B GLN* 3.6 42.8 - - + +
616B SER 5.1 0.7 - - - -
617B GLY* 1.3 72.3 - - - -
619B ASP* 1.3 65.6 + - - +
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Residues in contact with ASP 619 (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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330B TRP* 4.7 5.6 - - + -
431B ARG* 3.1 27.8 + - + +
432B PHE 3.3 4.0 - - - +
433B ARG* 3.3 27.2 + - - +
598B LEU 3.2 6.2 - - - +
599B LEU* 3.5 1.9 - - - -
600B ILE* 2.4 53.3 + - + +
602B GLN* 2.9 34.7 + - - +
617B GLY 4.4 0.3 - - - +
618B TRP* 1.3 82.6 - - - +
620B VAL* 1.3 63.0 + - - +
621B LEU* 3.7 3.0 + - + +
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Residues in contact with VAL 620 (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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431B ARG* 3.9 1.5 - - - -
432B PHE* 3.0 30.7 + - + +
434B LEU* 3.7 26.9 - - + -
443B LEU* 4.0 14.1 - - + -
447B ILE* 5.0 11.2 - - + -
597B ILE* 4.3 18.8 - - + -
598B LEU 3.3 6.7 - - - +
599B LEU* 3.7 20.0 - - + -
619B ASP* 1.3 71.2 - - - +
621B LEU* 1.3 61.7 + - - +
622B LEU* 3.8 29.5 - - + +
630B PHE* 6.1 0.2 - - + -
634B PHE* 5.5 4.7 - - + -
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Residues in contact with LEU 621 (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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311B ILE* 6.1 0.2 - - + -
328B TRP* 3.6 29.4 - - + -
330B TRP* 4.1 23.1 - - + +
429B MET* 3.9 22.7 - - + -
430B ASN 3.4 20.6 - - - +
431B ARG* 4.4 13.0 - - + +
553B ILE* 3.9 12.6 - - + +
597B ILE* 3.3 9.5 - - - +
598B LEU* 2.9 63.4 + - + +
600B ILE* 5.8 1.3 - - + -
619B ASP* 3.7 3.7 + - + +
620B VAL* 1.3 69.8 - - - +
622B LEU* 1.3 62.0 + - - +
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Residues in contact with LEU 622 (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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429B MET* 3.2 8.1 - - - +
430B ASN* 3.0 43.5 + - + +
432B PHE* 3.6 35.4 - - + -
553B ILE* 5.8 2.5 - - - -
597B ILE* 3.7 12.3 - - + +
620B VAL* 3.8 23.6 - - + +
621B LEU* 1.3 76.0 - - - +
623B PRO* 1.4 89.8 - - + +
626B TRP* 3.3 23.1 - - + +
630B PHE* 3.8 26.9 - - + -
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Residues in contact with PRO 623 (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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428B GLU 4.7 0.4 - - - +
429B MET* 3.9 12.6 - - + -
430B ASN* 4.0 2.6 + - - -
553B ILE* 4.4 17.9 - - + -
559B CYS* 4.0 25.6 - - - -
562B VAL* 4.2 27.8 - - + -
563B THR* 4.8 3.1 - - - +
595B ILE* 5.0 4.3 - - + -
596B PRO 4.2 14.6 - - - +
622B LEU* 1.4 107.3 - - + +
624B LYS* 1.3 65.4 + - - +
625B GLY 3.5 4.4 + - - +
626B TRP* 3.8 14.7 + - + -
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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