Contacts of the strand formed by residues 599 - 608 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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591B CYS* 3.4 21.1 - - - -
592B LEU 3.2 4.9 - - - +
593B LYS* 4.0 34.3 - - + +
597B GLY 3.4 9.7 + - - +
598B VAL* 1.3 78.9 - - - +
600B ILE* 1.3 65.2 + - - +
618B ILE* 3.8 2.1 - - - -
619B VAL* 3.0 39.7 + - + +
620B TYR* 2.9 28.3 + - + +
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Residues in contact with ILE 600 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591B CYS* 3.5 1.1 - - - -
592B LEU* 2.8 44.9 + - + +
594B PHE* 3.3 33.4 - - + -
598B VAL* 4.1 4.9 - - + -
599B GLN* 1.3 79.4 - - - +
601B GLN* 1.3 72.2 + - - +
602B LEU* 3.7 1.9 + - + -
616B THR* 4.4 10.3 - - + -
617B SER 3.5 10.5 - - - +
618B ILE* 3.9 12.3 - - + -
619B VAL* 4.3 2.5 - - - -
630B ALA* 3.2 33.2 - - + -
686B VAL* 4.2 14.4 - - + -
688B LEU* 3.7 14.8 - - + -
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Residues in contact with GLN 601 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589B SER* 5.3 10.4 + - - -
590B MET 3.6 9.4 - - - +
591B CYS* 4.6 5.2 - - + +
600B ILE* 1.3 75.6 - - - +
602B LEU* 1.3 66.4 + - - +
603B GLY* 4.1 1.2 - - - +
615B TYR* 3.7 23.5 - - - +
616B THR* 3.2 7.3 - - - -
617B SER* 2.9 39.4 + - - +
619B VAL* 3.2 30.0 - - + +
664B PRO* 5.3 6.9 - - - +
667B CYS* 5.4 1.4 - - - -
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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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589B SER* 3.4 4.9 - - - -
590B MET* 2.9 46.4 + - + +
592B LEU* 4.3 11.2 - - + -
600B ILE* 3.7 4.0 + - + +
601B GLN* 1.3 75.0 - - - +
603B GLY* 1.3 58.8 + - - +
604B PHE* 3.7 19.8 - - + -
614B ILE* 3.3 25.8 - - + -
615B TYR 3.6 1.3 - - - +
616B THR* 3.2 28.9 - - + -
632B VAL* 4.6 1.3 - - + -
684B PHE* 3.8 30.3 - - + -
686B VAL* 4.2 15.3 - - + -
705B VAL* 4.4 6.5 - - + -
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Residues in contact with GLY 603 (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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589B SER* 3.9 12.3 - - - -
601B GLN* 4.1 2.6 - - - +
602B LEU* 1.3 74.2 - - - +
604B PHE* 1.3 66.8 + - - -
614B ILE* 3.4 7.3 - - - +
615B TYR* 3.0 57.8 + - - -
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Residues in contact with PHE 604 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586B LEU* 3.5 16.8 - - + +
587B PRO* 3.6 31.4 - - + +
588B GLU 3.3 22.2 - - - -
589B SER* 4.3 2.8 + - - +
590B MET* 4.0 4.9 - - + -
602B LEU* 3.7 37.7 - - + -
603B GLY* 1.3 77.2 - - - -
605B ALA* 1.3 59.9 + - - +
612B MET* 3.9 26.2 - - + -
613B ILE 3.4 5.2 - - - -
614B ILE* 3.9 21.3 - - + -
615B TYR* 4.0 7.5 + - - -
684B PHE* 4.1 19.7 - + - -
707B VAL* 3.9 24.9 - - + -
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Residues in contact with ALA 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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586B LEU* 4.1 3.1 - - - -
604B PHE* 1.3 76.0 - - - +
606B ALA* 1.3 61.4 + - - +
612B MET* 3.2 8.9 - - - +
613B ILE* 2.8 46.9 + - + +
615B TYR* 4.5 1.8 - - + +
658B LEU* 4.6 8.7 - - + -
663B LEU* 3.6 30.5 - - + -
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Residues in contact with ALA 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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367B TYR* 5.5 1.6 + - - -
586B LEU* 3.8 14.4 - - + +
605B ALA* 1.3 73.9 - - - +
607B GLU* 1.3 60.0 + - - +
608B PHE 4.2 6.1 - - - +
611B VAL 3.9 3.6 - - - -
658B LEU* 4.4 9.1 - - - +
711B LEU* 4.0 30.3 - - + -
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Residues in contact with GLU 607 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B LEU* 4.4 0.5 - - - +
367B TYR* 3.5 28.2 - - + -
382B SER* 4.9 0.9 + - - -
605B ALA 3.8 0.4 + - - -
606B ALA* 1.3 74.2 - - - +
608B PHE* 1.3 86.2 + - + +
611B VAL* 2.8 17.6 + - + +
613B ILE* 3.7 8.4 - - + +
656B SER* 2.9 24.0 + - - -
657B TYR* 3.1 22.9 + - + +
658B LEU* 4.2 19.5 - - + -
671B ARG* 3.1 37.8 + - - -
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Residues in contact with PHE 608 (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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363B LEU* 3.3 35.0 - - + -
366B VAL* 3.7 15.9 - - + -
367B TYR* 3.8 17.7 - + + -
382B SER* 3.7 24.9 - - - +
384B LEU* 3.4 46.9 - - + -
606B ALA* 4.2 3.9 - - - +
607B GLU* 1.3 115.2 + - + +
609B SER* 1.3 64.1 + - - +
610B ASN* 3.0 17.3 - - - +
611B VAL* 3.1 27.7 + - + +
711B LEU* 3.6 9.0 - - - +
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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