Contacts of the strand formed by residues 599 - 608 (chain C) in PDB entry 3UO8
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 GLN 599 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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591C CYS* 3.6 24.6 - - - -
592C LEU 3.2 5.8 - - - +
593C LYS* 4.1 30.6 - - + +
597C GLY 3.5 8.6 + - - +
598C VAL* 1.3 81.5 - - - +
600C ILE* 1.3 63.0 + - - +
601C GLN 4.2 0.7 + - - -
617C SER 4.2 5.7 - - - +
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Residues in contact with ILE 600 (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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591C CYS* 3.6 2.4 - - - -
592C LEU* 2.8 47.5 + - + +
594C PHE* 3.0 44.0 - - + -
598C VAL* 3.7 18.2 - - + -
599C GLN* 1.3 76.1 - - - +
601C GLN* 1.3 69.7 + - - +
602C LEU* 3.8 2.2 + - + -
616C THR* 4.1 20.9 - - + -
617C SER 3.4 13.2 - - - +
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Residues in contact with GLN 601 (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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589C SER* 4.5 18.4 + - - -
590C MET 3.6 8.9 - - - +
591C CYS* 4.3 13.6 - - + +
599C GLN 4.1 1.0 + - - -
600C ILE* 1.3 73.5 - - - +
602C LEU* 1.3 67.1 + - - +
603C GLY* 4.9 1.1 - - - +
615C TYR* 3.7 3.5 - - + +
616C THR* 3.2 8.0 - - - -
617C SER* 2.9 42.1 + - - +
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Residues in contact with LEU 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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589C SER* 3.4 7.3 - - - -
590C MET* 2.8 67.4 + - + +
592C LEU* 4.6 18.2 - - + -
600C ILE* 4.9 3.4 - - + +
601C GLN* 1.3 75.9 - - - +
603C GLY* 1.3 58.8 + - - +
604C PHE* 3.9 17.3 - - + -
614C ILE* 3.6 22.2 - - + -
615C TYR 3.6 0.9 - - - +
616C THR* 3.2 28.9 - - + -
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Residues in contact with GLY 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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589C SER* 4.3 10.1 - - - -
601C GLN* 4.1 2.6 - - - +
602C LEU* 1.3 74.1 - - - +
604C PHE* 1.3 73.7 + - - -
614C ILE* 3.5 6.1 - - - +
615C TYR* 2.9 54.0 + - - -
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Residues in contact with PHE 604 (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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586C LEU* 3.5 26.1 - - + +
587C PRO* 3.6 46.9 - - + +
588C GLU 3.3 22.4 - - - -
589C SER* 4.5 2.3 + - - -
590C MET* 4.3 9.6 - - - -
602C LEU* 3.9 32.1 - - + -
603C GLY* 1.3 81.8 - - - -
605C ALA* 1.3 61.0 - - - +
612C MET* 3.8 13.9 - - + -
613C ILE 3.2 7.4 - - - +
614C ILE* 3.9 26.2 - - + -
615C TYR* 3.5 12.3 + - - -
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Residues in contact with ALA 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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586C LEU* 3.6 7.6 - - - -
604C PHE* 1.3 74.1 - - - +
606C ALA* 1.3 62.6 + - - +
612C MET* 3.4 5.0 - - - +
613C ILE* 2.8 49.3 + - + +
615C TYR* 4.4 10.3 - - + +
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Residues in contact with ALA 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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367C TYR* 5.0 5.9 + - - -
584C HIS* 4.9 21.8 - - + +
586C LEU* 3.2 31.7 - - + +
605C ALA* 1.3 74.4 - - - +
607C GLU* 1.3 62.3 + - - +
608C PHE 4.8 6.7 - - - +
611C VAL 4.0 4.3 - - - +
613C ILE* 5.8 0.2 - - - -
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Residues in contact with GLU 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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363C LEU* 4.2 17.1 - - + +
367C TYR* 3.4 32.8 - - + -
382C SER* 4.8 0.7 + - - -
384C LEU* 5.8 0.3 - - - +
605C ALA 3.9 0.4 + - - -
606C ALA* 1.3 73.5 - - - +
608C PHE* 1.3 95.9 + - + +
611C VAL* 3.0 26.1 + - + +
613C ILE* 3.5 30.0 - - + +
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Residues in contact with PHE 608 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363C LEU* 3.3 44.9 - - + -
366C VAL* 3.6 27.4 - - + -
367C TYR* 3.6 18.2 - + + -
382C SER* 3.5 26.9 - - - +
383C LEU 5.0 0.2 - - - -
384C LEU* 4.3 16.4 - - + -
606C ALA* 4.8 6.7 - - - +
607C GLU* 1.3 110.7 + - + +
609C SER* 1.3 67.6 + - - +
610C ASN* 3.0 13.9 - - - +
611C VAL* 3.0 32.1 + - + +
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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