Contacts of the helix formed by residues 713 - 726 (chain C) in PDB entry 5Y7K
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 PHE 713 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238C TYR* 6.2 2.4 - - + +
704C HIS* 3.7 40.7 + + + -
705C GLY 3.6 24.7 - - - +
706C THR* 3.9 23.3 + - + +
708C ASP* 4.1 5.1 + - - +
711C VAL 3.5 2.0 + - - -
712C HIS* 1.3 71.5 - - - +
714C GLN* 1.3 63.2 + - - +
715C GLN 3.0 1.4 + - - -
716C SER* 3.1 4.0 + - - -
717C ALA* 3.0 35.8 + - + -
734C TRP* 3.9 14.6 - - + -
241D TYR* 4.2 13.2 - + - -
706D THR* 5.1 3.6 - - + -
713D PHE* 6.0 3.6 - + - -
734D TRP* 3.8 39.9 - + + -
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Residues in contact with GLN 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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258C LYS* 3.0 26.9 + - - -
661C TYR* 3.1 38.0 + - + +
712C HIS* 2.9 10.1 + - + +
713C PHE* 1.3 78.5 - - - +
715C GLN* 1.3 62.0 + - - +
717C ALA* 3.8 7.4 - - - +
718C GLN* 3.1 29.8 + - + +
241D TYR* 4.6 17.3 - - + +
246D LEU 3.4 7.3 + - - -
247D GLN 2.8 24.8 + - - +
249D PRO* 3.6 30.0 - - + +
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Residues in contact with GLN 715 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655C PRO 3.3 16.4 - - - +
656C VAL* 3.7 10.4 - - - +
657C SER* 2.7 55.6 + - - +
658C ARG 3.2 8.1 + - - -
661C TYR* 3.4 32.9 + - + +
662C TYR* 3.8 23.8 - - - +
704C HIS* 4.4 0.2 - - + -
711C VAL* 3.6 19.9 - - + +
712C HIS* 2.7 28.9 + - + +
714C GLN* 1.3 74.3 - - + +
716C SER* 1.3 60.4 + - - +
718C GLN* 3.5 0.9 + - - +
719C ILE* 3.3 16.1 + - - +
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Residues in contact with SER 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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655C PRO* 3.1 19.9 - - - +
702C LEU* 3.4 26.5 - - - +
704C HIS* 2.6 43.0 + - - +
713C PHE* 3.1 3.6 + - - -
715C GLN* 1.3 76.4 - - - +
717C ALA* 1.3 64.4 + - - +
719C ILE* 3.2 9.3 + - - -
720C SER* 3.0 20.3 + - - -
734D TRP* 3.6 7.6 - - - -
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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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713C PHE* 3.0 25.3 + - + +
714C GLN 3.8 3.1 - - - +
716C SER* 1.3 78.8 - - - +
718C GLN* 1.3 57.6 + - - +
720C SER* 2.7 20.5 + - - -
721C LYS* 3.0 10.7 + - - +
241D TYR* 3.1 43.7 - - + +
734D TRP* 3.8 5.1 - - - +
736D THR* 2.8 14.6 + - - +
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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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661C TYR* 3.6 20.9 + - + +
689C MET* 3.1 32.0 - - + +
714C GLN* 3.1 19.8 + - + +
715C GLN 3.9 3.8 - - - +
717C ALA* 1.3 74.1 - - - +
719C ILE* 1.3 65.0 + - - +
721C LYS* 3.2 26.5 + - - +
722C ALA* 3.1 16.6 + - - +
241D TYR* 3.6 22.5 + - + +
242D SER 3.2 22.6 + - - -
243D ASP 3.5 11.5 + - - -
244D GLU* 3.8 16.2 - - + +
246D LEU 5.2 0.6 + - - -
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Residues in contact with ILE 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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637C SER* 4.6 1.3 - - - +
655C PRO* 4.1 25.4 - - + -
657C SER* 3.4 27.6 - - - -
688C VAL* 3.4 28.7 - - + -
689C MET* 3.8 6.5 - - - -
695C PHE* 5.6 2.0 - - + -
700C TYR* 4.1 30.3 - - + +
702C LEU* 4.1 6.5 - - + -
715C GLN 3.3 13.0 - - - +
716C SER* 3.2 10.5 + - - +
718C GLN* 1.3 76.4 - - - +
720C SER* 1.3 66.1 + - - +
722C ALA* 3.2 4.4 + - - +
723C LEU* 3.0 30.6 + - + +
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Residues in contact with SER 720 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702C LEU* 4.3 1.5 - - - +
716C SER 3.0 9.7 + - - -
717C ALA 2.7 21.7 + - - -
719C ILE* 1.3 76.6 - - - +
721C LYS* 1.3 63.1 + - - +
723C LEU* 3.2 3.7 + - - +
724C VAL* 3.0 29.1 + - - +
730C PHE* 3.7 28.4 - - - -
734D TRP* 2.9 38.8 + - - -
736D THR* 3.3 4.7 + - - -
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Residues in contact with LYS 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 ALA 3.0 12.1 + - - +
718C GLN* 3.2 26.5 + - - +
720C SER* 1.3 81.2 + - - +
722C ALA* 1.3 62.7 + - - +
724C VAL* 3.3 8.0 + - + +
725C ASP* 3.0 42.0 + - - +
242D SER 3.3 22.8 + - - -
243D ASP* 4.0 14.6 + - - +
244D GLU* 4.1 3.6 - - - +
736D THR* 3.5 38.8 - - + +
737D ASP* 3.8 6.1 - - + +
738D GLU* 5.8 1.3 - - - +
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Residues in contact with ALA 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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689C MET* 3.6 39.3 - - + +
692C ALA* 3.8 6.0 - - + +
718C GLN 3.1 18.5 + - - +
719C ILE* 3.6 3.6 - - + +
721C LYS* 1.3 77.2 - - - +
723C LEU* 1.3 62.0 + - - +
725C ASP* 3.2 18.9 + - - +
726C VAL* 3.3 17.3 + - - +
244D GLU* 5.7 0.2 - - - +
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Residues in contact with LEU 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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692C ALA* 3.5 36.8 - - + +
695C PHE* 3.8 20.9 - - + -
700C TYR* 3.8 26.9 - - + -
719C ILE* 3.0 24.6 + - + +
720C SER 3.2 5.4 + - - +
722C ALA* 1.3 76.9 - - - +
724C VAL* 1.3 61.3 + - - +
726C VAL* 3.3 4.1 + - - +
727C GLY 3.0 4.0 + - - -
728C VAL* 2.8 36.5 + - + +
730C PHE* 3.5 42.6 - - + -
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Residues in contact with VAL 724 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720C SER* 3.0 24.4 + - - +
721C LYS* 3.6 7.9 - - + +
723C LEU* 1.3 77.1 - - - +
725C ASP* 1.3 64.8 + - - +
727C GLY* 3.0 13.0 + - - -
730C PHE* 4.4 3.8 - - + -
735D TYR* 3.8 18.8 - - + -
736D THR 6.3 0.4 - - - +
746D THR* 3.6 19.1 - - - +
747D ALA* 3.6 38.1 - - + +
750D HIS* 3.8 31.3 - - + +
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Residues in contact with ASP 725 (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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721C LYS* 3.0 33.5 + - - +
722C ALA* 3.2 12.3 + - - +
724C VAL* 1.3 79.4 - - - +
726C VAL* 1.3 60.5 + - + +
727C GLY 3.6 0.5 + - - -
746D THR* 3.6 32.1 + - + +
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Residues in contact with VAL 726 (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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692C ALA* 3.7 19.7 - - + +
693C GLU* 3.8 26.9 - - + +
696C LYS* 3.7 18.9 + - - -
722C ALA 3.3 17.0 - - - +
723C LEU* 3.4 9.0 - - - +
725C ASP* 1.3 80.6 - - + +
727C GLY* 1.3 62.7 + - - +
728C VAL* 3.4 19.2 + - + -
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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