Contacts of the helix formed by residues 713 - 721 (chain C) in PDB entry 2W4T
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 TYR 713 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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503C GLU 2.1 29.9 + - - -
711C LEU 3.3 2.2 + - - -
712C ILE* 1.3 69.6 - - - +
714C SER* 1.3 55.5 + - - +
716C PHE* 3.6 8.9 - - - -
717C LYS* 2.8 33.8 + - - +
735C GLY* 3.4 19.8 - - - +
736C LYS* 3.4 32.1 - - + +
739C SER* 2.8 27.1 - - - -
740C GLU* 4.4 9.3 + - - -
755C LEU* 2.5 12.3 + - - +
756C GLY 3.1 3.0 + - - -
757C THR 3.7 8.5 - - - -
758C THR* 2.9 23.9 + - - +
759C LYS* 3.0 24.7 - - - -
760C VAL* 3.1 25.1 - - + +
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Residues in contact with SER 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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712C ILE* 2.7 24.1 + - - +
713C TYR* 1.3 78.3 - - - +
715C GLU* 1.3 78.0 + - - +
717C LYS* 4.3 3.0 - - - +
718C GLN* 3.6 17.7 + - - +
735C GLY* 5.2 4.5 - - - -
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Residues in contact with GLU 715 (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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712C ILE* 2.6 42.4 + - + -
714C SER* 1.3 83.8 + - - +
716C PHE* 1.3 57.9 + - - +
717C LYS 3.5 0.2 - - - -
718C GLN* 4.0 8.5 - - - +
719C ARG* 2.5 54.3 + - - +
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Residues in contact with PHE 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 LEU* 3.6 26.2 - - + -
712C ILE 2.9 11.4 + - - +
713C TYR* 3.2 12.5 + - - +
715C GLU* 1.3 76.0 - - - +
717C LYS* 1.3 62.3 + - - +
718C GLN 3.2 0.2 - - - -
719C ARG* 3.2 6.4 + - - +
720C TYR* 2.8 60.4 + + + +
739C SER* 3.5 24.2 - - - -
742C ILE* 3.4 43.1 - - + -
743C LEU* 4.1 2.7 - - + -
760C VAL* 4.1 5.4 - - + -
762C PHE* 3.4 35.0 - + - -
767C LEU* 4.9 0.4 - - + -
770C LEU* 4.3 5.8 - - + -
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Residues in contact with LYS 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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713C TYR 2.8 16.8 + - - +
714C SER* 4.3 3.8 - - - +
716C PHE* 1.3 81.9 - - - +
718C GLN* 1.3 63.4 + - - +
720C TYR 5.2 0.2 - - - -
721C SER* 2.3 48.2 + - - +
728C ILE* 4.6 23.9 - - - +
734C ASP 5.4 1.1 - - - +
735C GLY* 4.0 8.3 - - - -
738C VAL* 2.5 59.8 - - + +
742C ILE* 5.9 3.5 - - + +
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Residues in contact with GLN 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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714C SER 3.6 15.8 + - - +
715C GLU* 4.0 11.7 - - - +
716C PHE 3.2 0.6 - - - -
717C LYS* 1.3 81.9 - - - +
719C ARG* 1.3 71.0 + - + +
721C SER* 4.8 2.7 + - - -
722C ILE* 5.3 5.2 - - - +
91Z LYS* 3.9 30.3 - - - +
92Z THR* 6.2 3.2 - - - +
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Residues in contact with ARG 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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711C LEU* 2.4 58.2 - - - +
715C GLU* 2.5 35.9 + - - +
716C PHE* 3.2 2.2 + - - +
718C GLN* 1.3 92.3 - - - +
720C TYR* 1.3 73.0 + - + +
721C SER 3.7 1.1 - - - -
722C ILE* 2.9 20.0 - - - +
774C ARG* 3.5 31.5 - - - +
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Residues in contact with TYR 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 LEU* 4.8 5.8 - - + -
716C PHE* 2.8 61.0 + + + +
717C LYS* 3.9 1.8 - - - -
719C ARG* 1.3 91.1 - - + +
721C SER* 1.3 61.8 + - - +
722C ILE* 3.4 4.7 - - - -
723C LEU* 3.8 31.7 - - + +
742C ILE* 3.9 19.5 - - + +
767C LEU* 3.4 20.4 + - + +
770C LEU* 3.0 42.4 - - + +
771C GLU* 3.2 25.6 + - - +
774C ARG* 4.1 14.3 + - + -
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Residues in contact with SER 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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717C LYS* 2.3 47.1 + - - +
718C GLN* 5.3 1.8 - - - -
719C ARG 3.7 1.4 - - - -
720C TYR* 1.3 74.0 - - - +
722C ILE* 1.3 54.8 + - - +
723C LEU 2.5 20.3 + - - -
724C ALA 3.1 13.7 + - - -
725C PRO* 3.4 13.5 - - - +
728C ILE* 4.8 12.1 - - - +
742C ILE* 4.7 10.6 - - - +
88Z GLU* 4.5 12.3 - - - -
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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