Contacts of the helix formed by residues 699 - 714 (chain A) 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 699 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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595A LEU* 4.6 4.9 - - + +
599A ALA* 4.0 15.5 - - + -
600A ASP* 4.4 12.1 - - + +
603A PHE* 3.6 61.0 - - + -
693A LEU* 3.8 12.8 - - + -
696A TYR* 3.1 20.7 + - + +
697A PRO 3.0 0.2 + - - -
698A MET* 1.3 100.6 - - + +
700A ARG* 1.3 67.9 + - - +
701A ARG 3.3 0.9 - - - -
702A ALA* 3.3 16.4 + - - +
703A PHE* 3.4 14.5 - - + -
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Residues in contact with ARG 700 (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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663A LEU 4.4 1.4 + - - -
664A LEU* 3.4 43.6 + - + +
689A PHE* 4.1 4.9 - - - -
690A ASN* 3.8 19.4 + - - -
693A LEU* 3.6 34.2 - - + +
697A PRO* 3.2 15.1 + - + +
699A MET* 1.3 78.7 - - - +
701A ARG* 1.3 65.3 + - - +
702A ALA 3.0 1.2 + - - -
703A PHE* 3.1 14.5 + - - +
704A GLU* 3.2 38.9 + - + +
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Residues in contact with ARG 701 (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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697A PRO 4.7 0.6 + - - -
698A MET* 4.3 13.5 + - - +
699A MET 3.3 1.2 - - - -
700A ARG* 1.3 76.3 - - - +
702A ALA* 1.3 59.4 + - - +
704A GLU* 2.9 19.5 + - + +
705A THR* 2.9 39.1 + - - +
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Residues in contact with ALA 702 (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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595A LEU* 3.5 28.3 - - + -
657A TYR* 3.7 2.8 + - - +
698A MET 5.1 1.5 + - - +
699A MET* 3.3 8.1 + - - +
700A ARG 3.0 1.4 + - - -
701A ARG* 1.3 79.9 - - - +
703A PHE* 1.3 62.9 + - - +
705A THR* 3.8 7.4 + - - -
706A VAL* 3.5 24.1 + - - +
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Residues in contact with PHE 703 (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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595A LEU* 3.3 35.2 - - + -
603A PHE* 4.7 6.7 - + - -
607A MET* 4.1 19.3 - - + -
632A MET* 3.6 28.9 - - + -
634A PHE* 4.3 2.5 - + - -
657A TYR* 3.8 21.8 - + - -
660A GLU* 4.4 5.9 - - + +
664A LEU* 4.3 9.6 - - + -
689A PHE* 3.9 33.0 - + + -
693A LEU* 4.1 15.3 - - + -
699A MET 3.4 26.0 - - - -
700A ARG* 3.1 8.1 + - - +
702A ALA* 1.3 78.6 - - - +
704A GLU* 1.3 56.4 + - - +
706A VAL* 3.2 4.5 + - - +
707A ALA* 2.9 29.3 + - - +
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Residues in contact with GLU 704 (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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664A LEU* 4.2 20.6 - - + -
700A ARG* 3.3 45.8 + - + +
701A ARG* 2.9 19.9 + - + +
703A PHE* 1.3 73.8 - - - +
705A THR* 1.3 55.1 + - - +
707A ALA* 3.6 0.9 - - - +
708A LEU* 2.8 50.4 + - + +
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Residues in contact with THR 705 (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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701A ARG* 2.9 28.6 + - - +
702A ALA* 3.9 8.2 - - - -
704A GLU* 1.3 71.9 - - - +
706A VAL* 1.3 67.5 + - + +
708A LEU* 3.9 8.0 - - - +
709A ASP* 3.0 24.8 + - + +
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Residues in contact with VAL 706 (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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657A TYR* 3.3 37.7 - - + +
660A GLU* 4.1 1.1 - - - +
702A ALA 3.5 8.4 + - - +
703A PHE 3.2 6.0 + - - +
705A THR* 1.3 83.8 - - + +
707A ALA* 1.3 56.9 + - - +
709A ASP* 3.3 7.0 - - - +
710A ARG* 3.0 66.6 + - - +
728A GOL 4.3 11.4 - - - +
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Residues in contact with ALA 707 (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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660A GLU* 3.9 12.8 - - + -
661A ILE* 3.8 24.1 - - + +
664A LEU* 3.7 23.6 - - + -
703A PHE 2.9 16.1 + - - +
704A GLU 4.0 2.2 - - - +
706A VAL* 1.3 72.6 - - - +
708A LEU* 1.3 67.1 + - + +
710A ARG* 3.9 1.6 - - - +
711A LEU* 3.1 31.0 + - + +
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Residues in contact with LEU 708 (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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704A GLU* 2.8 39.8 + - + +
705A THR* 3.9 6.5 - - - +
707A ALA* 1.3 71.7 - - + +
709A ASP* 1.3 67.6 + - - +
711A LEU* 3.2 15.6 + - + +
712A ASP* 2.9 33.8 + - - +
717A LYS* 6.4 2.2 - - - -
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Residues in contact with ASP 709 (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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705A THR* 3.0 15.3 + - + +
706A VAL* 3.3 12.3 - - - +
708A LEU* 1.3 78.2 - - - +
710A ARG* 1.3 60.8 + - - +
712A ASP* 3.4 11.6 + - - +
713A ARG* 3.2 57.4 + - - +
728A GOL 3.3 8.1 + - - +
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Residues in contact with ARG 710 (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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652A LEU* 3.9 10.5 - - - +
656A SER* 4.6 1.6 + - - -
657A TYR* 2.7 32.3 + - - +
658A PHE* 3.8 0.8 - - - +
660A GLU* 2.9 36.4 + - - -
661A ILE* 4.2 11.2 - - + -
706A VAL* 3.0 25.0 + - - +
707A ALA 4.2 0.7 - - - +
708A LEU 3.2 0.2 - - - -
709A ASP* 1.3 78.9 - - - +
711A LEU* 1.3 63.7 + - - +
713A ARG* 3.3 7.2 + - - +
714A ILE* 3.2 27.4 + - - +
728A GOL 2.9 52.3 + - - +
846A CMP 3.4 52.6 + - + +
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Residues in contact with LEU 711 (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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661A ILE* 4.1 33.6 - - + +
665A THR* 4.9 10.1 - - + -
670A THR* 4.1 12.3 - - + -
707A ALA* 3.1 25.9 + - + +
708A LEU* 3.2 16.4 + - + +
710A ARG* 1.3 73.2 - - - +
712A ASP* 1.3 64.9 + - - +
714A ILE* 3.9 3.5 - - + -
715A GLY* 3.1 3.8 + - - -
716A LYS* 3.0 66.8 + - + +
717A LYS* 5.5 6.1 - - + -
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Residues in contact with ASP 712 (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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708A LEU* 2.9 24.1 + - - +
709A ASP* 3.4 14.1 - - - +
710A ARG 3.3 0.2 - - - -
711A LEU* 1.3 76.9 - - - +
713A ARG* 1.3 60.3 + - + +
715A GLY* 2.9 22.4 + - - -
716A LYS 5.4 0.9 - - - +
717A LYS* 5.3 8.5 - - - -
639B VAL* 5.3 1.6 - - - +
677B THR* 3.6 8.5 - - - +
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Residues in contact with ARG 713 (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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649A GLU* 4.2 11.2 + - - +
650A THR* 4.1 16.0 - - - +
709A ASP* 3.2 29.5 + - - +
710A ARG* 3.3 7.2 + - - +
712A ASP* 1.3 76.1 - - + +
714A ILE* 1.3 60.3 + - - +
715A GLY 3.6 0.3 + - - -
728A GOL 3.1 39.3 + - - -
846A CMP 3.4 38.8 + - - +
677B THR* 3.9 11.7 - - - +
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Residues in contact with ILE 714 (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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644A THR* 4.6 11.0 - - + +
649A GLU* 3.2 41.1 - - + +
661A ILE* 5.3 0.2 - - + -
670A THR* 3.3 46.4 - - - +
710A ARG 3.2 14.7 + - - +
711A LEU* 4.2 10.1 - - + +
713A ARG* 1.3 74.7 - - - +
715A GLY* 1.3 61.9 + - - +
716A LYS* 3.9 11.5 - - + +
846A CMP 3.7 23.6 - - + +
637B HIS* 3.3 20.3 + - - -
677B THR* 4.4 4.7 + - - -
678B TYR 5.6 0.2 - - - +
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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