Contacts of the helix formed by residues 705 - 718 (chain A) in PDB entry 3II5
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 LEU 705 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567A HIS* 5.3 1.6 - - - +
634A PHE* 3.5 42.0 - - + -
635A GLN* 4.1 26.2 - - - +
638A VAL* 4.3 3.6 - - + -
703A ARG 4.8 1.8 - - - +
704A PRO* 1.3 79.0 - - - +
706A PHE* 1.3 61.0 + - - +
707A PRO* 3.4 11.2 - - + -
708A GLN* 3.1 13.5 + - + +
709A ILE* 3.0 27.7 + - - +
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Residues in contact with PHE 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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560A ALA* 3.9 21.3 - - + -
563A MET* 3.5 38.4 - - + -
564A ASP* 3.8 23.3 - - + -
567A HIS* 3.3 41.4 + + + +
637A ASP 4.4 0.4 - - - -
638A VAL* 3.8 22.0 - - + -
641A PHE* 4.0 35.2 - + + -
705A LEU* 1.3 69.9 - - - +
707A PRO* 1.3 67.7 - - + +
709A ILE* 4.0 14.4 - - + -
710A LEU* 2.6 38.0 + - - +
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Residues in contact with PRO 707 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564A ASP* 3.7 22.8 - - - +
567A HIS* 6.6 0.2 - - + -
705A LEU* 3.5 11.9 - - + -
706A PHE* 1.3 91.9 - - + +
708A GLN* 1.3 57.0 + - + +
710A LEU* 3.7 3.3 - - + +
711A ALA* 2.9 30.5 + - - +
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Residues in contact with GLN 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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694A GLU* 5.4 4.4 + - - -
704A PRO* 3.7 30.2 - - + +
705A LEU* 3.1 12.4 + - + +
707A PRO* 1.3 79.8 - - + +
709A ILE* 1.3 57.7 + - - +
711A ALA* 3.5 7.6 - - - +
712A SER* 3.0 33.9 + - - +
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Residues in contact with ILE 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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560A ALA* 4.5 1.1 - - + -
638A VAL* 3.9 28.9 - - + -
641A PHE* 3.8 24.7 - - + -
691A LEU* 4.1 16.4 - - + -
695A CYS* 3.9 9.6 - - - -
704A PRO* 4.0 15.5 - - + +
705A LEU 3.0 22.6 + - - +
706A PHE* 3.5 31.2 - - + +
708A GLN* 1.3 75.4 - - - +
710A LEU* 1.3 68.1 + - - +
712A SER* 2.9 8.5 + - - -
713A ILE* 2.9 32.9 + - + +
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Residues in contact with LEU 710 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A ARG* 3.9 30.1 - - + +
560A ALA* 3.9 16.4 - - + +
561A GLN* 4.1 22.4 - - + +
564A ASP* 3.4 33.0 - - + +
706A PHE 2.6 22.4 + - - +
707A PRO* 3.7 3.6 - - + +
709A ILE* 1.3 73.3 - - - +
711A ALA* 1.3 62.1 + - - +
713A ILE* 3.3 3.1 + - + +
714A GLU* 3.0 52.4 + - - +
476B HIS* 4.9 6.5 - - - -
477B GLY 4.9 1.8 - - - +
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Residues in contact with ALA 711 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
707A PRO 2.9 18.3 + - - +
708A GLN* 3.5 9.0 - - - +
710A LEU* 1.3 77.6 - - - +
712A SER* 1.3 62.6 + - - +
714A GLU* 3.2 10.9 + - - +
715A LEU* 3.0 26.8 + - - +
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Residues in contact with SER 712 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691A LEU* 4.1 26.5 - - - +
694A GLU* 5.7 0.2 + - - -
708A GLN* 3.0 19.2 + - - +
709A ILE 2.9 9.6 + - - -
711A ALA* 1.3 75.6 - - - +
713A ILE* 1.3 61.1 + - - +
715A LEU* 3.8 9.5 - - - +
716A LEU* 3.1 30.7 + - - +
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Residues in contact with ILE 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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553A ILE* 4.2 18.8 - - + +
556A ALA* 4.0 27.1 - - + +
557A ARG* 3.8 28.3 - - + +
560A ALA* 4.0 17.9 - - + -
641A PHE* 4.1 8.7 - - + -
645A LEU* 5.4 1.1 - - + -
688A MET* 4.9 7.9 - - + -
691A LEU* 3.9 16.2 - - + -
709A ILE* 2.9 25.3 + - + +
710A LEU* 3.8 5.8 - - - +
711A ALA 3.2 0.2 - - - -
712A SER* 1.3 75.0 - - - +
714A GLU* 1.3 60.1 + - - +
716A LEU* 3.2 9.1 + - + +
717A ALA* 2.9 32.2 + - + +
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Residues in contact with GLU 714 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A ARG* 4.2 20.1 - - - +
561A GLN* 4.4 6.2 - - - +
710A LEU* 3.0 44.0 + - + +
711A ALA* 3.8 10.8 - - - +
713A ILE* 1.3 75.6 - - - +
715A LEU* 1.3 63.0 + - - +
717A ALA* 3.4 13.6 + - - +
718A ARG* 3.5 39.4 + - - +
474B LYS* 4.3 21.9 + - - +
477B GLY* 5.3 2.6 + - - -
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Residues in contact with LEU 715 (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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711A ALA 3.0 17.3 + - - +
712A SER* 3.8 8.7 - - - +
714A GLU* 1.3 79.9 - - - +
716A LEU* 1.3 60.4 + - - +
717A ALA 3.4 0.5 + - - -
718A ARG* 3.6 30.7 + - + +
719A SER* 3.9 7.6 + - - -
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Residues in contact with LEU 716 (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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553A ILE* 4.3 21.1 - - + +
685A PRO* 4.7 13.6 - - + +
687A ALA* 4.0 23.6 - - + +
688A MET* 4.0 53.4 - - + +
691A LEU* 5.1 3.4 - - + -
712A SER* 3.1 22.9 + - - +
713A ILE* 3.2 16.3 + - + +
715A LEU* 1.3 77.6 - - + +
717A ALA* 1.3 63.8 + - - +
718A ARG 3.4 0.8 + - - -
719A SER* 3.7 18.8 + - - -
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Residues in contact with ALA 717 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553A ILE* 4.3 20.4 - - + -
557A ARG* 5.6 7.9 - - - +
713A ILE* 2.9 19.2 + - + +
714A GLU* 3.6 9.4 - - - +
715A LEU 3.2 0.4 - - - -
716A LEU* 1.3 80.4 - - - +
718A ARG* 1.3 63.9 + - + +
719A SER 3.1 12.0 + - - -
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Residues in contact with ARG 718 (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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711A ALA 5.6 0.2 + - - -
714A GLU* 3.5 30.1 + - - +
715A LEU* 3.6 34.4 + - - +
716A LEU 3.4 1.0 - - - -
717A ALA* 1.3 76.4 - - + +
719A SER* 1.3 58.2 + - - +
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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