Contacts of the strand formed by residues 605 - 612 (chain A) in PDB entry 4X7J
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 605 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601A ARG* 3.4 5.4 - - - +
602A GLY 3.1 32.9 + - - -
603A GLY 3.3 1.3 - - - +
604A PHE* 1.3 80.6 - - - +
606A VAL* 1.3 64.3 + - - +
607A VAL* 5.4 0.9 - - - -
622A LYS* 4.6 9.6 - - - -
623A ARG 3.2 11.7 - - - -
624A ILE* 4.2 8.7 - - - +
957A GLY 5.7 0.7 - - - -
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Residues in contact with VAL 606 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598A CYS* 3.9 14.6 - - - -
600A GLY 3.6 12.1 - - - +
601A ARG* 4.1 26.9 - - + +
604A PHE 5.7 0.4 - - - +
605A GLY* 1.3 78.4 - - - +
607A VAL* 1.3 63.6 - - - +
608A PHE* 3.6 31.8 - - + -
621A ILE 3.7 0.9 - - - +
622A LYS* 3.4 1.0 - - - -
623A ARG* 2.7 60.1 + - - +
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Residues in contact with VAL 607 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598A CYS* 3.7 4.7 - - - -
599A LEU* 2.8 46.4 + - + -
600A GLY 2.9 14.0 + - - +
605A GLY 5.4 0.7 - - - -
606A VAL* 1.3 77.5 - - - +
608A PHE* 1.3 61.7 + - - +
620A ALA* 4.4 0.4 - - + -
621A ILE 3.3 13.0 - - - +
622A LYS* 4.0 26.9 - - + -
956A PHE 4.1 8.5 - - - +
957A GLY 4.7 4.0 - - - +
958A LEU* 3.8 25.1 - - + -
1101A 3Z1 3.7 27.4 - - + -
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Residues in contact with PHE 608 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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589A TYR* 3.4 36.3 - + + +
595A PRO* 5.7 4.7 - - + -
597A GLN 3.4 7.0 - - - +
598A CYS* 4.0 24.5 - - + -
599A LEU* 3.9 5.0 - - - +
601A ARG* 5.9 0.4 - - - -
606A VAL* 3.6 34.1 - - + -
607A VAL* 1.3 74.4 - - - +
609A GLU* 1.3 63.0 + - - +
610A ALA 3.9 0.3 + - - -
619A TYR 3.6 0.3 - - - +
620A ALA* 3.5 4.0 - - - -
621A ILE* 2.8 43.5 + - + +
623A ARG* 3.9 36.3 - - + -
885A TYR* 5.7 0.9 - + - -
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Residues in contact with GLU 609 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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595A PRO* 3.8 1.4 - - - +
596A ILE* 2.8 42.2 + - + +
597A GLN* 2.8 50.2 + - + +
599A LEU* 3.7 17.9 - - + +
608A PHE* 1.3 73.3 - - - +
610A ALA* 1.3 63.3 + - - +
618A ASN* 2.9 23.4 - - + +
619A TYR 3.4 6.5 - - - +
890A LEU* 3.6 29.2 - - + +
893A LYS* 5.2 0.9 - - - -
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Residues in contact with ALA 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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589A TYR* 3.9 24.2 - - + +
593A PHE* 4.0 22.9 - - + -
594A GLU 3.5 12.8 - - - +
595A PRO* 4.0 2.2 - - + -
596A ILE* 3.8 6.3 - - - -
608A PHE 3.9 0.4 + - - +
609A GLU* 1.3 76.6 - - - +
611A LYS* 1.3 61.3 + - - +
612A ASN 3.9 0.9 + - - -
619A TYR* 2.9 35.3 + - - +
621A ILE* 4.2 7.4 - - + -
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Residues in contact with LYS 611 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593A PHE* 3.1 6.1 - - - -
594A GLU* 2.8 68.8 + - + +
596A ILE* 3.4 9.0 - - + +
610A ALA* 1.3 72.1 - - - +
612A ASN* 1.3 74.1 + - - +
613A LYS* 3.6 3.3 + - - +
616A ASP* 3.4 33.4 - - - +
617A CYS 3.4 7.6 - - - +
618A ASN* 3.1 35.9 + - - +
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Residues in contact with ASN 612 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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592A ASP* 3.4 19.0 - - - +
593A PHE* 3.7 31.0 - - + -
610A ALA 3.9 0.2 + - - -
611A LYS* 1.3 74.5 - - - +
613A LYS* 1.3 58.7 + - - +
614A VAL* 3.2 16.0 - - - +
615A ASP* 2.9 53.5 + - - +
616A ASP* 2.8 31.4 + - - -
617A CYS 2.9 8.3 + - - -
619A TYR* 3.9 6.3 - - + -
887A GLN* 5.5 1.1 - - - -
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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