Contacts of the helix formed by residues 706 - 719 (chain A) in PDB entry 3C4C
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 SER 706 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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635A PHE* 5.9 9.2 - - - -
636A GLN* 6.4 2.0 - - - -
639A VAL* 4.4 6.7 - - - -
704A ARG 3.8 2.9 + - - -
705A PRO* 1.3 75.3 - - - +
707A PHE* 1.3 63.9 + - - +
708A PRO* 3.8 10.2 - - - +
709A ARG* 3.6 12.7 + - - +
710A ILE* 3.2 19.3 + - - +
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Residues in contact with PHE 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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561A ALA* 3.9 28.0 - - + -
564A MET* 3.4 36.3 - - + -
565A ASP* 3.8 17.5 - - - +
568A HIS* 3.4 35.3 + + + +
638A ASP 4.4 2.9 - - - -
639A VAL* 3.8 30.3 - - + -
642A PHE* 3.8 26.5 - + + -
706A SER* 1.3 74.4 - - - +
708A PRO* 1.3 76.6 - - + +
710A ILE* 3.0 23.4 + - + +
711A LEU* 2.9 24.5 + - - +
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Residues in contact with PRO 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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565A ASP* 3.4 25.7 - - - +
568A HIS* 6.3 0.4 - - + -
706A SER* 4.0 9.0 - - - +
707A PHE* 1.3 88.8 - - + +
709A ARG* 1.3 58.5 - - - +
711A LEU* 3.2 4.5 + - + +
712A ALA* 2.9 24.9 + - - +
477B HIS* 6.2 0.9 - - + -
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Residues in contact with ARG 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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692A LEU* 5.2 0.3 - - - +
704A ARG 5.7 0.8 + - - -
705A PRO* 4.1 25.8 - - + +
706A SER* 3.6 16.8 + - - +
707A PHE 3.3 0.4 - - - -
708A PRO* 1.3 75.5 - - - +
710A ILE* 1.3 67.0 + - - +
712A ALA* 3.4 9.3 - - + +
713A GLU* 3.2 25.6 + - - +
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Residues in contact with ILE 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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561A ALA* 4.2 2.2 - - + -
639A VAL* 3.8 9.4 - - + -
642A PHE* 4.2 12.6 - - + -
692A LEU* 4.4 12.3 - - + +
696A CYS* 3.7 20.9 - - - -
705A PRO* 3.5 37.5 - - + +
706A SER 3.2 16.5 + - - +
707A PHE* 3.0 37.8 + - + +
709A ARG* 1.3 75.4 - - - +
711A LEU* 1.3 59.9 + - - +
713A GLU* 3.9 1.4 + - - +
714A ILE* 3.0 50.3 + - + +
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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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558A ARG* 4.6 4.0 - - + +
561A ALA* 4.2 17.0 - - + +
562A ARG* 3.8 19.3 - - + -
565A ASP* 3.2 31.2 - - + +
707A PHE 2.9 10.7 + - - +
708A PRO 3.5 8.1 - - - +
710A ILE* 1.3 74.5 - - - +
712A ALA* 1.3 67.8 + - - +
714A ILE* 4.4 6.1 - - + -
715A GLU* 3.5 41.9 + - + +
477B HIS* 4.1 23.3 - - - +
478B GLY 4.4 1.6 - - - +
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Residues in contact with ALA 712 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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708A PRO 2.9 12.6 + - - +
709A ARG* 3.4 14.1 - - + +
710A ILE 3.3 0.2 - - - -
711A LEU* 1.3 80.9 - - - +
713A GLU* 1.3 67.2 + - - +
715A GLU* 4.0 0.9 - - - +
716A GLU* 2.9 30.8 + - + +
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Residues in contact with GLU 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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688A ARG* 2.6 56.8 + - - +
692A LEU* 4.0 25.6 + - + +
709A ARG 3.2 11.7 + - - +
710A ILE 4.3 0.2 - - - +
711A LEU 3.7 0.2 - - - -
712A ALA* 1.3 76.5 - - - +
714A ILE* 1.3 57.8 + - - +
716A GLU* 4.4 7.8 + - - +
717A LEU* 2.8 33.0 + - - +
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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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554A ILE* 4.4 13.4 - - + +
557A ALA* 4.4 6.3 - - + +
558A ARG* 3.7 34.3 - - + +
561A ALA* 4.0 10.8 - - + -
642A PHE* 3.9 17.5 - - + -
689A MET* 5.0 4.5 - - + -
692A LEU* 3.2 29.6 - - + -
710A ILE* 3.0 35.1 + - + +
711A LEU* 4.7 4.3 - - + +
712A ALA 3.0 1.6 + - - -
713A GLU* 1.3 72.3 - - - +
715A GLU* 1.3 66.4 + - + +
717A LEU* 3.4 10.1 - - + +
718A ALA* 3.0 22.3 + - - +
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Residues in contact with GLU 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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558A ARG* 3.1 28.7 + - + +
562A ARG* 3.3 24.4 + - - -
711A LEU* 3.5 35.6 + - + +
712A ALA* 3.2 3.1 + - - +
714A ILE* 1.3 78.2 - - - +
716A GLU* 1.3 58.5 + - - +
718A ALA* 3.1 25.5 + - - +
719A ARG* 3.9 7.3 + - - +
475B LYS* 2.6 40.9 + - - +
478B GLY* 4.2 4.7 - - - -
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Residues in contact with GLU 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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688A ARG* 3.2 29.7 + - - -
712A ALA* 2.9 22.1 + - + +
713A GLU* 3.6 11.0 + - - +
715A GLU* 1.3 77.5 - - + +
717A LEU* 1.3 56.8 + - - +
719A ARG* 3.2 45.2 + - - +
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Residues in contact with LEU 717 (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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554A ILE* 4.4 13.2 - - + -
686A PRO* 4.3 22.9 - - + -
688A ARG* 3.6 35.0 - - + +
689A MET* 4.2 18.2 - - + +
692A LEU* 5.0 3.1 - - + -
713A GLU* 2.8 34.0 + - - +
714A ILE* 3.4 20.4 - - + +
716A GLU* 1.3 75.3 - - - +
718A ALA* 1.3 68.2 + - - +
719A ARG 2.9 19.9 + - - +
720A GLU* 3.0 24.6 + - - +
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Residues in contact with ALA 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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554A ILE* 4.7 12.1 - - + -
558A ARG* 4.3 24.7 - - - +
714A ILE 3.0 14.4 + - - +
715A GLU* 3.1 19.5 + - - +
717A LEU* 1.3 81.8 - - - +
719A ARG* 1.3 54.1 + - - +
720A GLU* 3.4 19.3 - - - +
721A LEU* 3.7 12.0 + - - +
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Residues in contact with ARG 719 (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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688A ARG* 4.1 8.4 + - - +
715A GLU 3.9 6.9 + - - +
716A GLU* 3.2 52.0 + - - +
717A LEU* 2.9 14.2 - - - +
718A ALA* 1.3 73.4 - - - +
720A GLU* 1.3 65.9 + - - +
721A LEU* 5.7 3.8 - - + -
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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