Contacts of the strand formed by residues 599 - 606 (chain A) in PDB entry 4NPJ
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 ASP 599 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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565A SER 3.6 6.6 - - - +
566A VAL* 3.7 16.5 - - - +
567A GLY 4.3 3.1 + - - -
597A ARG 3.8 9.2 - - - +
598A GLN* 1.3 80.8 - - - +
600A LEU* 1.3 62.7 + - - +
601A GLU* 3.6 5.1 + - + +
617A LYS* 3.5 43.2 + - + +
618A VAL 3.7 5.4 - - - +
619A PRO* 3.4 22.4 - - - +
620A LEU* 4.6 0.4 - - - -
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Residues in contact with LEU 600 (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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538A LEU* 4.2 8.5 - - + -
540A LEU* 3.7 27.4 - - + -
564A MET* 4.2 9.9 - - + -
565A SER 3.6 15.7 - - - +
566A VAL* 4.2 10.8 - - + -
590A PHE* 5.1 1.6 - - + -
599A ASP* 1.3 71.5 - - - +
601A GLU* 1.3 70.0 + - - +
602A VAL* 3.9 21.1 - - + -
616A LEU 3.6 1.4 - - - +
617A LYS* 3.4 3.3 - - - +
618A VAL* 2.8 48.8 + - + +
620A LEU* 4.0 15.5 - - + +
648A MET* 5.2 1.6 - - - -
650A ILE* 4.1 27.1 - - + -
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Residues in contact with GLU 601 (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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563A GLN 3.6 1.6 - - - +
564A MET* 3.3 4.7 - - - -
565A SER* 2.8 49.9 + - - +
599A ASP* 3.6 3.1 + - + +
600A LEU* 1.3 74.2 - - - +
602A VAL* 1.3 69.9 + - - +
603A GLU* 4.2 4.7 - - + +
615A ASN* 5.7 6.3 - - + -
616A LEU 3.6 5.6 - - - +
617A LYS* 3.0 35.8 + - + +
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Residues in contact with VAL 602 (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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562A VAL* 3.7 24.5 - - + -
563A GLN 3.6 2.9 - - - -
564A MET* 4.0 11.9 - - + -
600A LEU* 3.9 23.6 - - + +
601A GLU* 1.3 80.0 - - - +
603A GLU* 1.3 64.7 + - - +
604A VAL* 4.9 2.2 - - + -
615A ASN* 3.1 7.0 - - - +
616A LEU* 2.8 53.5 + - + +
618A VAL* 5.6 0.4 - - + -
637A LEU* 5.5 0.4 - - + -
646A ILE* 4.2 9.4 - - + -
648A MET* 3.8 31.9 - - + -
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Residues in contact with GLU 603 (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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561A VAL 3.7 0.9 - - - +
562A VAL* 3.4 3.2 - - - -
563A GLN* 2.9 46.0 + - + +
601A GLU* 4.2 5.3 - - + -
602A VAL* 1.3 74.3 - - - +
604A VAL* 1.3 65.5 + - - +
605A ARG* 3.5 35.0 + - + +
611A CYS 5.6 0.2 - - - -
612A SER* 4.0 20.5 + - - -
614A GLY 3.9 4.0 - - - +
615A ASN* 4.1 16.3 + - + +
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Residues in contact with VAL 604 (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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545A ALA* 5.8 0.4 - - + -
548A LEU* 4.2 17.3 - - + -
560A PRO* 4.3 8.1 - - + -
561A VAL 3.4 9.2 - - - +
562A VAL* 4.4 11.4 - - + +
584A TRP* 4.5 3.1 - - + -
602A VAL* 4.9 3.1 - - + -
603A GLU* 1.3 74.7 - - - +
605A ARG* 1.3 57.9 + - - +
612A SER* 3.5 5.0 + - - -
613A LEU* 2.6 53.2 + - + +
614A GLY 2.9 17.8 + - - +
637A LEU* 4.2 26.0 - - + -
646A ILE* 4.2 18.8 - - + -
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Residues in contact with ARG 605 (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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560A PRO* 3.3 5.4 - - - +
561A VAL* 2.8 49.4 + - + +
563A GLN* 3.7 28.9 + - - +
572A GLU* 4.5 6.8 + - - -
603A GLU* 3.5 39.8 + - + +
604A VAL* 1.3 73.0 - - - +
606A ASP* 1.3 63.9 + - - +
607A GLU* 3.7 0.7 - - - -
610A GLN* 2.6 46.6 + - - +
611A CYS 3.3 11.7 - - - +
612A SER* 4.5 0.7 - - - -
613A LEU* 3.5 5.4 - - - +
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Residues in contact with ASP 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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558A PRO* 3.5 24.8 - - + +
559A ASN 2.6 27.0 + - - -
605A ARG* 1.3 71.4 - - - +
607A GLU* 1.3 55.4 + - - +
608A GLN* 3.1 15.5 + - - +
609A HIS* 2.8 35.1 + - - -
610A GLN* 2.6 36.0 + - - -
611A CYS* 2.9 22.0 + - - +
613A LEU* 3.6 14.6 - - + +
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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