Contacts of the strand formed by residues 601 - 607 (chain B) in PDB entry 4A9C
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 HIS 601 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553B THR* 3.6 20.6 - - + -
554B SER 3.3 2.4 + - - -
555B PHE* 3.4 21.3 - + + +
556B GLY 2.9 24.8 + - - +
599B PHE* 4.0 1.7 - - - +
600B THR* 1.3 89.1 - - + +
602B LEU* 1.3 60.3 + - - +
603B PHE* 4.1 13.1 - - + -
695B LYS 3.8 3.1 - - - -
696B SER* 2.8 21.7 + - - +
700B THR* 3.5 30.0 - - - -
701B HIS 4.1 3.6 - - - -
702B ILE* 3.5 18.5 - - + +
727B VAL* 3.5 28.1 - - + +
728B GLY 3.8 10.1 + - - -
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Residues in contact with LEU 602 (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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556B GLY* 3.4 15.9 - - - +
558B VAL* 4.2 22.0 - - + -
585B LEU* 5.8 0.2 - - + -
595B ILE* 3.7 23.3 - - + +
596B SER* 3.9 15.9 - - - +
599B PHE* 3.7 33.1 + - + +
601B HIS* 1.3 73.9 - - - +
603B PHE* 1.3 63.7 + - - +
604B TRP* 4.2 8.6 + - + +
650B PHE* 3.7 29.2 - - + -
694B TRP* 3.2 5.2 - - - +
695B LYS* 2.8 46.7 + - + +
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Residues in contact with PHE 603 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B VAL* 4.9 2.9 - - + -
428B ILE* 3.6 13.9 - - + -
555B PHE* 4.3 7.4 - + - -
556B GLY 2.7 12.5 + - - -
557B PHE* 3.4 44.5 - + + -
558B VAL* 2.8 32.7 + - - +
601B HIS* 4.1 20.9 - - + -
602B LEU* 1.3 76.4 - - - +
604B TRP* 1.3 55.1 + - - +
605B PHE* 3.7 11.3 - - + -
692B ILE* 4.9 2.5 - - + -
693B LEU 3.5 4.5 - - - +
694B TRP* 3.6 23.3 - - + -
702B ILE* 3.6 21.3 - - + -
725B PHE* 3.6 34.1 - + - -
727B VAL* 4.2 10.8 - - + -
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Residues in contact with TRP 604 (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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558B VAL* 3.5 23.5 - - + +
560B CYS* 3.5 22.9 - - - -
562B LEU* 5.7 0.8 - - + +
576B TYR* 3.6 39.0 - + - -
579B ILE* 3.6 41.5 - - + -
580B LEU* 3.7 27.4 - - + -
595B ILE* 3.7 14.1 - - + -
602B LEU* 4.2 5.3 + - + -
603B PHE* 1.3 71.2 - - - +
605B PHE* 1.3 69.2 + - - +
608B LEU* 4.3 2.5 - - + -
647B PHE* 3.4 30.8 - + + -
650B PHE* 3.9 22.9 - + + -
691B ARG 4.2 0.5 - - - +
692B ILE 3.7 0.2 - - - -
693B LEU* 2.7 45.1 + - + +
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Residues in contact with PHE 605 (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 ILE* 3.7 22.0 - - + -
429B GLY 4.5 0.2 - - - -
430B THR* 4.3 7.0 - - - -
468B VAL* 3.7 22.7 - - + -
470B GLY* 3.7 22.0 - - - -
510B VAL* 3.9 8.3 - - + -
557B PHE* 3.9 21.8 - + + -
558B VAL 2.8 20.5 + - - +
559B ASN* 3.3 24.4 - - + -
560B CYS* 3.0 27.2 + - - -
603B PHE* 3.7 21.3 - - + -
604B TRP* 1.3 79.6 - - - +
606B GLY* 1.3 61.1 + - - +
608B LEU* 4.0 7.0 - - - -
691B ARG 3.2 14.8 - - - +
692B ILE* 3.9 17.0 - - + -
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Residues in contact with GLY 606 (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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430B THR* 3.0 22.9 + - - -
472B GLN* 3.4 8.7 - - - -
559B ASN* 3.6 2.7 - - - -
560B CYS 3.3 9.0 - - - -
605B PHE* 1.3 80.1 - - - +
607B ASP* 1.3 61.3 + - - -
608B LEU* 3.2 9.7 + - - +
690B ASP* 3.4 3.6 - - - -
691B ARG 3.3 22.5 + - - -
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Residues in contact with ASP 607 (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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432B ASN* 2.8 24.8 + - - -
472B GLN* 3.4 21.1 - - + +
560B CYS 2.8 9.3 + - - -
561B HIS* 3.4 24.0 + - + -
562B LEU 3.0 24.8 + - - -
606B GLY* 1.3 67.8 - - - -
608B LEU* 1.4 59.4 + - - +
609B ASN* 3.1 22.7 + - - +
689B CYS* 3.3 17.8 - - - +
690B ASP* 3.8 11.9 - - - +
718B HIS* 3.4 11.3 + - - -
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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