Contacts of the helix formed by residues 713 - 723 (chain A) in PDB entry 4PE5
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 713 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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482A GLY* 4.7 9.4 - - - -
684A VAL* 3.8 14.9 - - - +
711A TYR* 3.5 19.0 - - - +
712A GLU* 1.3 79.3 - - - +
714A ALA* 1.3 62.7 + - - +
715A ALA* 3.7 8.4 + - - +
716A GLU* 3.5 29.7 + - - +
717A ALA* 3.8 4.5 + - - +
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Residues in contact with ALA 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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405A GLN* 3.9 25.1 - - - +
406A GLU* 6.2 1.6 - - + +
484A PHE* 6.1 0.8 - - + -
684A VAL* 3.7 20.4 - - + +
713A SER* 1.3 75.6 - - - +
715A ALA* 1.3 59.8 + - - +
716A GLU 3.4 0.2 - - - -
717A ALA* 3.3 1.6 + - - +
718A ILE* 2.9 43.1 + - + +
729A PHE* 4.3 8.3 - - + -
731A TRP* 4.2 12.8 - - + +
735A VAL* 5.6 0.2 - - + -
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Residues in contact with ALA 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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713A SER* 3.4 8.9 - - - +
714A ALA* 1.3 79.0 - - - +
716A GLU* 1.3 59.4 + - + +
718A ILE* 3.9 6.5 - - - +
719A GLN* 2.9 31.2 + - - +
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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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711A TYR* 4.0 27.7 - - + -
712A GLU* 4.4 16.3 + - - +
713A SER* 3.5 20.3 + - - +
714A ALA 3.4 0.4 - - - -
715A ALA* 1.3 79.0 - - + +
717A ALA* 1.3 56.2 + - - +
719A GLN* 3.6 6.5 + - - +
720A ALA* 2.9 28.2 + - - +
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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
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683A THR 5.2 0.7 - - - +
684A VAL* 5.2 0.2 - - + -
711A TYR* 3.7 28.0 - - + -
713A SER 3.8 9.7 + - - +
714A ALA 3.3 7.4 + - - +
715A ALA 3.2 0.4 - - - -
716A GLU* 1.3 77.8 - - - +
718A ILE* 1.3 59.5 + - - +
720A ALA* 3.1 3.6 + - - +
721A VAL* 2.9 30.4 + - - +
726A LEU* 3.8 4.8 - - + +
729A PHE* 3.5 36.5 - - + -
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Residues in contact with ILE 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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406A GLU* 4.9 6.1 - - + -
541A LEU* 4.3 8.3 - - + -
714A ALA* 2.9 26.9 + - + +
715A ALA* 3.9 6.3 - - - +
717A ALA* 1.3 75.2 - - - +
719A GLN* 1.3 59.0 + - - +
721A VAL* 3.2 9.5 - - - +
722A ARG* 2.9 30.4 + - + +
729A PHE* 4.0 18.6 - - + -
735A VAL* 4.6 11.9 - - + -
736A LEU* 5.0 0.9 - - + -
739A GLU* 3.6 39.3 - - + +
746A LEU* 3.7 24.7 - - + -
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Residues in contact with GLN 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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715A ALA 2.9 19.0 + - - +
716A GLU* 3.8 7.4 - - - +
718A ILE* 1.3 77.8 - - - +
720A ALA* 1.3 57.1 + - - +
722A ARG* 3.7 22.1 + - - +
723A ASP* 2.9 63.2 + - - +
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Residues in contact with ALA 720 (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 TYR* 3.3 30.7 - - + +
716A GLU 2.9 19.5 + - - +
717A ALA 3.1 6.3 + - - +
719A GLN* 1.3 74.4 - - - +
721A VAL* 1.3 59.1 + - - +
722A ARG 3.1 1.8 - - - -
723A ASP* 3.1 8.1 + - - -
725A LYS* 2.7 43.8 + - + +
726A LEU* 3.9 6.7 - - + -
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Residues in contact with VAL 721 (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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541A LEU* 3.9 34.3 - - + +
542A VAL* 4.2 1.3 - - - -
543A LYS* 3.7 33.5 - - + +
717A ALA 2.9 14.5 + - - +
718A ILE* 3.2 20.2 - - - +
720A ALA* 1.3 76.3 - - - +
722A ARG* 1.3 59.5 + - - +
724A ASN* 3.7 7.7 + - - -
726A LEU* 3.9 35.6 - - + +
727A HIS 4.4 0.4 - - - -
728A ALA* 4.3 4.9 - - - +
729A PHE* 4.8 4.9 - - + -
746A LEU* 3.9 15.1 - - + +
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Residues in contact with ARG 722 (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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543A LYS* 5.7 1.1 - - - +
718A ILE* 2.9 19.7 + - - +
719A GLN* 3.7 25.4 + - - +
720A ALA 3.1 0.2 - - - -
721A VAL* 1.3 79.0 - - - +
723A ASP* 1.3 62.6 + - - +
724A ASN* 3.2 12.3 + - - +
743A LYS* 5.0 11.8 - - - +
745A ASP* 3.3 35.1 + - - +
746A LEU* 3.9 20.6 - - + +
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Residues in contact with ASP 723 (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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719A GLN* 2.9 46.8 + - - +
720A ALA* 3.1 3.9 + - - +
722A ARG* 1.3 83.1 - - - +
724A ASN* 1.3 72.1 + - - +
725A LYS* 3.2 6.1 + - + +
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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