Contacts of the helix formed by residues 698 - 715 (chain B) in PDB entry 3U11
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 MET 698 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603B PHE* 6.0 0.9 - - + -
696B TYR* 3.5 42.8 - - + +
697B PRO* 1.3 78.9 - - + +
699B MET* 1.3 68.5 + - - +
700B ARG 3.3 0.7 - - - -
701B ARG* 3.3 22.4 + - + +
702B ALA* 3.3 12.0 + - - +
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Residues in contact with MET 699 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595B LEU* 3.5 43.3 - - + -
603B PHE* 3.7 31.6 - - + -
607B MET* 4.4 10.3 - - + -
692B VAL* 4.6 11.2 - - + -
693B LEU* 3.6 23.6 - - + -
696B TYR* 3.0 20.1 + - + +
697B PRO 3.0 1.2 - - - -
698B MET* 1.3 83.3 - - - +
700B ARG* 1.3 66.8 + - - +
702B ALA* 3.4 15.6 + - + +
703B PHE* 3.3 32.8 + - + -
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Residues in contact with ARG 700 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663B LEU 5.9 0.6 + - - -
664B LEU* 3.7 39.6 + - + +
666B ARG* 4.9 12.4 - - - +
689B PHE* 5.6 1.2 - - - -
690B ASN* 5.6 3.2 + - - -
693B LEU* 3.6 36.5 - - + +
697B PRO 3.7 10.8 + - - +
699B MET* 1.3 77.3 - - - +
701B ARG* 1.3 58.5 + - - +
703B PHE* 2.9 22.5 + - - +
704B GLU* 2.9 39.8 + - - +
722B LEU* 5.4 3.8 - - - -
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Residues in contact with ARG 701 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697B PRO 4.8 0.2 + - - -
698B MET* 3.3 19.7 + - + +
700B ARG* 1.3 77.8 - - - +
702B ALA* 1.3 62.2 + - - +
704B GLU* 3.2 24.4 + - + +
705B THR* 3.2 28.5 + - - +
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Residues in contact with ALA 702 (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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595B LEU* 4.1 25.3 - - + +
657B TYR* 3.8 4.7 + - - -
698B MET* 3.3 9.3 + - + +
699B MET* 3.7 17.0 - - + +
700B ARG 3.1 0.8 + - - -
701B ARG* 1.3 78.2 - - - +
703B PHE* 1.3 63.0 + - + +
705B THR* 4.9 2.8 - - - -
706B VAL* 3.6 21.5 + - - +
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Residues in contact with PHE 703 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595B LEU* 4.2 13.7 - - + -
607B MET* 5.3 3.4 - - + -
632B MET* 3.7 20.0 - - + -
634B PHE* 4.9 3.6 - + - -
657B TYR* 3.2 44.0 - + - -
660B GLU* 4.1 11.1 - - + +
664B LEU* 3.5 19.3 - - + -
684B LEU* 5.6 0.9 - - + -
689B PHE* 3.3 37.2 - + - -
693B LEU* 4.6 0.9 - - + -
699B MET* 3.3 45.5 + - + -
700B ARG* 2.9 5.2 + - - +
702B ALA* 1.3 79.0 - - - +
704B GLU* 1.3 56.6 + - - +
705B THR 3.3 0.4 - - - -
706B VAL* 3.2 3.1 + - - +
707B ALA* 2.7 35.5 + - - +
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Residues in contact with GLU 704 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664B LEU* 3.9 11.2 - - + +
700B ARG* 2.9 45.4 + - + +
701B ARG* 3.2 21.8 + - + +
703B PHE* 1.3 75.8 - - - +
705B THR* 1.3 54.1 + - - +
707B ALA* 3.2 1.0 + - - +
708B LEU* 2.8 42.2 + - + +
719B SER 5.5 0.3 - - - +
720B ILE* 3.5 35.9 - - + +
722B LEU* 3.4 28.5 - - - +
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Residues in contact with THR 705 (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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701B ARG* 3.2 21.3 + - - +
702B ALA* 4.9 2.1 - - - -
703B PHE 3.3 0.4 - - - -
704B GLU* 1.3 79.2 - - - +
706B VAL* 1.3 67.2 + - + +
708B LEU* 3.5 9.2 + - - +
709B ASP* 3.1 23.9 + - - +
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Residues in contact with VAL 706 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657B TYR* 3.7 21.3 - - + +
660B GLU* 4.7 1.1 - - - +
702B ALA 3.6 17.0 - - - +
703B PHE 3.2 5.9 + - - +
705B THR* 1.3 76.8 - - + +
707B ALA* 1.3 67.1 + - - +
709B ASP* 3.5 5.9 + - - +
710B ARG* 3.0 55.1 + - + +
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Residues in contact with ALA 707 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660B GLU* 4.0 5.5 + - + +
661B ILE* 3.3 32.9 - - + +
664B LEU* 4.1 14.1 - - + -
703B PHE 2.7 22.3 + - - +
704B GLU 3.5 4.0 - - - +
706B VAL* 1.3 74.8 - - - +
708B LEU* 1.3 51.8 + - - +
710B ARG* 3.0 3.0 + - - +
711B LEU* 2.6 40.7 + - - +
720B ILE* 4.2 10.5 - - + -
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Residues in contact with LEU 708 (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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704B GLU* 2.8 27.2 + - + +
705B THR* 3.7 9.2 - - - +
707B ALA* 1.3 67.5 - - - +
709B ASP* 1.3 67.2 + - - +
711B LEU* 3.1 8.9 + - + +
712B ASP* 3.0 22.7 + - - +
717B LYS* 5.5 10.2 - - + +
718B ASN 5.0 8.7 - - - +
720B ILE* 3.5 39.5 - - + +
721B LEU* 3.6 42.4 - - + -
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Residues in contact with ASP 709 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705B THR* 3.1 14.7 + - + +
706B VAL* 3.8 6.5 - - - +
708B LEU* 1.3 79.5 - - - +
710B ARG* 1.3 56.5 + - - +
712B ASP* 3.2 13.1 - - - +
713B ARG* 3.0 59.5 + - - -
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Residues in contact with ARG 710 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652B LEU* 3.7 24.5 - - - +
656B SER* 4.7 3.0 + - - -
657B TYR* 2.8 38.8 + - - +
658B PHE* 4.1 0.2 - - - +
660B GLU* 2.9 36.1 + - - -
661B ILE* 4.4 1.3 - - + -
706B VAL* 3.0 34.3 + - + +
707B ALA* 3.0 10.1 + - - +
709B ASP* 1.3 73.6 - - + +
711B LEU* 1.3 59.2 + - - +
712B ASP 2.9 10.1 + - - -
713B ARG* 3.3 8.8 + - - +
714B ILE* 3.1 18.5 + - - +
846B CMP 3.4 67.7 + - + +
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Residues in contact with LEU 711 (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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661B ILE* 3.9 16.6 - - + -
670B THR* 3.8 35.9 - - + +
707B ALA 2.6 20.5 + - - +
708B LEU* 3.1 8.7 + - + +
710B ARG* 1.3 71.2 - - - +
712B ASP* 1.3 54.4 + - - +
714B ILE* 4.9 4.3 - - + -
715B GLY 3.2 3.5 + - - -
716B LYS* 2.4 68.3 + - + +
717B LYS* 4.6 6.0 - - + +
718B ASN* 4.3 16.4 - - + +
720B ILE* 3.6 28.5 - - + -
846B CMP 5.2 2.9 - - + +
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Residues in contact with ASP 712 (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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708B LEU 3.0 10.8 + - - +
709B ASP* 3.2 20.3 - - - +
710B ARG 2.9 1.6 - - - -
711B LEU* 1.3 76.4 - - - +
713B ARG* 1.3 65.2 + - - +
714B ILE 2.9 6.5 + - - +
715B GLY* 3.2 15.2 + - - -
717B LYS* 5.1 20.3 + - + +
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Residues in contact with ARG 713 (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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647B ASN* 4.1 0.5 - - - +
648B LYS* 2.5 54.2 - - + +
650B THR* 5.1 9.2 + - - +
709B ASP* 3.0 51.9 + - - +
710B ARG* 3.3 6.1 + - - +
712B ASP* 1.3 76.8 - - - +
714B ILE* 1.3 61.2 + - - +
846B CMP 3.8 30.4 + - - +
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Residues in contact with ILE 714 (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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642B VAL* 4.7 3.4 - - + -
644B THR* 3.5 25.4 - - + +
647B ASN* 2.2 41.8 + - - +
649B GLU* 4.9 9.6 - - + -
670B THR* 4.6 3.6 - - - +
671B ALA* 4.3 9.4 - - + -
710B ARG 3.1 9.1 + - - +
711B LEU* 4.7 5.2 - - + +
712B ASP 2.9 2.5 + - - -
713B ARG* 1.3 80.2 - - - +
715B GLY* 1.3 58.2 + - - +
716B LYS* 3.2 32.5 - - + -
846B CMP 3.0 44.2 - - + +
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Residues in contact with GLY 715 (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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711B LEU 3.2 6.0 + - - -
712B ASP* 3.4 10.5 - - - -
714B ILE* 1.3 80.3 - - - +
716B LYS* 1.3 65.8 + - - +
717B LYS* 4.3 1.3 - - - -
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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