Contacts of the helix formed by residues 713 - 723 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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482C GLY* 4.7 7.9 - - - -
684C VAL* 3.9 9.6 - - - +
711C TYR* 3.7 10.4 - - - +
712C GLU* 1.3 79.7 - - - +
714C ALA* 1.3 63.4 + - - +
715C ALA* 3.8 8.0 + - - +
716C GLU* 3.3 32.0 + - - +
717C ALA* 3.6 14.2 + - - +
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Residues in contact with ALA 714 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404C HIS 5.9 1.3 - - - +
405C GLN* 3.9 26.7 - - - +
406C GLU* 6.0 1.8 - - + +
484C PHE* 6.0 0.9 - - + -
684C VAL* 3.7 21.2 - - + +
713C SER* 1.3 73.4 - - - +
715C ALA* 1.3 60.0 + - - +
717C ALA* 3.2 4.3 + - - +
718C ILE* 2.9 43.1 + - + +
729C PHE* 4.4 4.7 - - + -
731C TRP* 4.2 12.1 - - + +
735C VAL* 5.6 0.4 - - + -
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Residues in contact with ALA 715 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404C HIS* 6.0 6.5 - - + +
713C SER* 3.3 8.8 - - - +
714C ALA* 1.3 77.9 - - - +
716C GLU* 1.3 58.2 + - + +
718C ILE* 3.4 9.0 + - - +
719C GLN* 2.9 30.9 + - - +
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Residues in contact with GLU 716 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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711C TYR* 4.0 24.2 - - + -
712C GLU* 4.4 15.0 + - - +
713C SER* 3.3 25.2 + - - +
714C ALA 3.3 0.4 - - - -
715C ALA* 1.3 79.1 - - + +
717C ALA* 1.3 57.0 + - - +
719C GLN* 3.7 6.5 - - - +
720C ALA* 2.9 27.9 + - - +
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Residues in contact with ALA 717 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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683C THR 5.3 0.4 - - - +
684C VAL* 5.1 0.9 - - + -
711C TYR* 3.9 24.8 - - + -
713C SER 3.6 10.5 + - - +
714C ALA 3.2 7.5 + - - +
716C GLU* 1.3 77.0 - - - +
718C ILE* 1.3 60.1 + - - +
720C ALA* 3.1 4.1 + - - +
721C VAL* 2.9 30.2 + - - +
726C LEU* 3.8 4.0 - - + +
729C PHE* 3.5 39.0 - - + -
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Residues in contact with ILE 718 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406C GLU* 4.7 7.2 - - + -
541C LEU* 4.4 9.0 - - + -
714C ALA* 2.9 28.6 + - + +
715C ALA* 3.8 7.2 - - - +
717C ALA* 1.3 74.1 - - - +
719C GLN* 1.3 57.9 + - - +
721C VAL* 3.2 9.3 - - - +
722C ARG* 2.9 33.1 + - + +
729C PHE* 4.1 15.7 - - + -
735C VAL* 4.6 12.6 - - + -
736C LEU* 5.2 0.9 - - + -
739C GLU* 3.7 37.2 - - + +
746C LEU* 3.7 25.1 - - + -
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Residues in contact with GLN 719 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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715C ALA 2.9 18.6 + - - +
716C GLU* 3.8 8.1 - - - +
718C ILE* 1.3 78.2 - - - +
720C ALA* 1.3 57.2 + - - +
722C ARG* 3.7 19.6 + - - +
723C ASP* 2.9 63.4 + - - +
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Residues in contact with ALA 720 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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711C TYR* 3.4 31.4 - - + +
716C GLU 2.9 18.7 + - - +
717C ALA 3.1 5.8 + - - +
719C GLN* 1.3 73.8 - - - +
721C VAL* 1.3 57.1 + - - +
722C ARG 3.1 4.3 - - - -
723C ASP* 3.3 6.7 + - - -
725C LYS* 2.7 40.6 + - + +
726C LEU* 3.8 10.1 - - + -
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Residues in contact with VAL 721 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541C LEU* 3.7 41.5 - - + +
542C VAL* 4.3 0.9 - - - -
543C LYS* 3.3 36.0 - - - +
717C ALA 2.9 13.8 + - - +
718C ILE* 3.2 20.6 - - - +
720C ALA* 1.3 76.9 - - - +
722C ARG* 1.3 57.6 + - - +
724C ASN* 3.9 5.2 + - - -
726C LEU* 3.9 33.9 - - + +
727C HIS 4.5 0.4 - - - -
728C ALA* 4.3 5.8 - - - +
729C PHE* 4.7 4.0 - - + -
746C LEU* 4.0 8.9 - - + +
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Residues in contact with ARG 722 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543C LYS* 5.3 2.2 - - - +
718C ILE* 2.9 20.1 + - - +
719C GLN* 3.7 24.6 + - - +
720C ALA 3.1 0.2 - - - -
721C VAL* 1.3 77.2 - - - +
723C ASP* 1.3 62.6 + - - +
724C ASN* 3.2 15.0 + - - +
742C GLN 5.8 0.4 + - - -
743C LYS* 4.9 12.1 - - - +
745C ASP* 3.3 34.0 + - - +
746C LEU* 3.9 21.4 - - + +
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Residues in contact with ASP 723 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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719C GLN* 2.9 48.0 + - - +
720C ALA* 3.3 3.7 + - - +
722C ARG* 1.3 83.9 - - - +
724C ASN* 1.3 72.1 + - - +
725C LYS* 3.2 6.3 + - + +
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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
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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