Contacts of the strand formed by residues 598 - 607 (chain C) in PDB entry 5IPN
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 VAL 598 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594C VAL* 3.9 0.2 - - - -
595C THR* 2.9 41.1 + - - +
596C ASP* 4.1 8.5 - - + +
597C GLY* 1.3 75.9 - - - +
599C VAL* 1.3 65.5 + - - +
600C THR* 3.4 10.3 + - - +
626C GLU* 5.4 6.3 - - + +
627C GLY* 3.2 21.3 - - - +
628C HIS* 5.3 3.6 - - + -
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Residues in contact with VAL 599 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592C ARG* 3.2 45.2 + - + +
593C LYS 3.9 4.0 - - - +
594C VAL* 3.8 23.3 - - + +
597C GLY 3.8 10.8 - - - +
598C VAL* 1.3 73.6 - - - +
600C THR* 1.3 63.5 + - - +
601C ASP* 4.0 3.8 + - - +
623C LEU* 4.0 26.4 - - + +
626C GLU* 6.1 1.2 - - - -
627C GLY 4.1 3.4 + - - +
628C HIS* 5.0 0.7 - - - -
629C PHE* 4.1 16.6 - - + -
653C MET* 3.8 14.6 - - + -
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Residues in contact with THR 600 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592C ARG* 3.9 13.9 + - - +
593C LYS 2.9 22.2 + - - +
595C THR* 3.8 15.1 + - - -
598C VAL* 3.7 9.3 + - - +
599C VAL* 1.3 77.2 - - - +
601C ASP* 1.3 68.6 + - + +
602C GLU* 3.3 44.1 + - + +
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Residues in contact with ASP 601 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C VAL* 4.1 24.9 - - + +
592C ARG* 3.8 15.9 + - - +
599C VAL 4.2 2.9 - - - +
600C THR* 1.3 78.8 - - + +
602C GLU* 1.3 64.3 + - - +
603C ILE* 3.5 17.1 + - - +
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Residues in contact with GLU 602 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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592C ARG* 3.6 4.0 - - - -
593C LYS* 3.1 53.4 + - + +
595C THR* 4.5 2.3 + - - -
600C THR* 3.5 32.3 + - + +
601C ASP* 1.3 79.6 - - - +
603C ILE* 1.3 61.5 + - - +
604C HIS* 3.5 26.1 + - - +
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Residues in contact with ILE 603 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C VAL* 4.4 12.8 - - + +
22C LEU* 3.8 40.6 - - + -
590C PRO* 3.7 28.5 - - + -
591C TYR 3.4 11.4 - - - +
592C ARG* 4.5 11.7 - - + -
601C ASP 3.5 12.3 + - - +
602C GLU* 1.3 81.2 - - - +
604C HIS* 1.3 73.2 + - - +
605C TYR* 4.3 15.9 + - + -
655C VAL* 4.4 4.5 - - + -
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Residues in contact with HIS 604 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591C TYR* 2.9 34.3 + - - +
593C LYS* 3.6 36.3 - - + +
602C GLU* 3.5 27.4 + - + +
603C ILE* 1.3 82.2 + - - +
605C TYR* 1.3 66.8 + - - +
606C LEU* 3.5 7.8 + - + +
652C TYR* 3.9 26.7 + + + +
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Residues in contact with TYR 605 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C LEU* 4.1 19.8 - - - +
578C TYR 4.3 0.7 - - - -
580C GLN* 3.3 44.5 + - + -
588C GLU* 3.5 36.9 - - + +
589C THR 3.5 4.0 - - - -
590C PRO* 3.3 35.2 - - + +
603C ILE* 4.3 15.9 - - + -
604C HIS* 1.3 74.7 - - - +
606C LEU* 1.3 64.0 + - - +
607C SER 4.1 0.7 + - - -
610C GLU* 4.1 6.4 - - - +
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Residues in contact with LEU 606 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557C ARG* 3.1 16.5 + - - -
588C GLU* 3.2 4.4 - - - -
589C THR 3.0 22.9 + - - -
591C TYR* 3.8 30.5 - - + -
604C HIS* 4.4 7.2 - - + +
605C TYR* 1.3 76.6 - - - +
607C SER* 1.3 67.5 + - - +
610C GLU* 3.6 29.2 - - + +
611C GLU* 4.1 19.1 - - - -
614C TYR* 4.6 9.0 - - + -
616C ILE* 4.4 6.7 - - + -
652C TYR* 4.3 38.6 - - + +
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Residues in contact with SER 607 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407C ARG* 5.5 0.3 + - - -
557C ARG* 3.1 5.5 + - - -
582C ASN* 4.7 17.5 - - - -
586C PHE* 5.1 6.7 - - - -
587C LEU 3.7 11.7 - - - -
588C GLU* 4.1 6.3 + - - +
605C TYR 4.1 0.8 + - - -
606C LEU* 1.3 76.7 - - - +
608C ALA* 1.3 65.5 + - - +
609C ILE* 3.7 11.4 + - - +
610C GLU* 3.4 35.2 + - - +
611C GLU* 3.0 18.4 + - - +
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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
------------------------------------------------------------
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