Contacts of the helix formed by residues 702 - 716 (chain H) in PDB entry 5G04
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 ASN 702 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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669H SER* 3.8 23.9 + - - +
670H VAL* 5.1 2.1 + - - +
673H CYS* 3.9 7.3 - - - -
695H ALA 5.8 0.2 - - - +
699H ASP* 4.0 13.4 + - + +
700H PRO 3.1 6.1 + - - -
701H LYS* 1.3 72.5 - - - +
703H PRO* 1.3 69.5 - - - +
704H LEU* 3.6 11.8 - - - +
705H CYS* 3.1 36.0 + - + +
706H LYS* 3.5 24.6 + - - +
729H LEU* 4.9 0.2 - - - +
732H ILE* 5.0 1.7 - - - +
180L TYR* 3.1 39.6 - - - -
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Residues in contact with PRO 703 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701H LYS 3.2 11.0 - - - +
702H ASN* 1.3 81.6 - - - +
704H LEU* 1.3 66.4 + - - +
705H CYS 3.3 0.3 + - - -
707H PHE* 3.1 21.5 + - - +
729H LEU* 3.4 18.0 - - + +
732H ILE* 4.6 2.2 - - + -
733H VAL* 3.4 27.8 - - + -
176L ASP* 3.6 21.8 - - + +
177L PHE* 3.4 22.2 - - + -
180L TYR* 3.5 27.4 - - + -
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Residues in contact with LEU 704 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670H VAL* 4.0 16.4 - - + +
673H CYS* 4.2 16.8 - - + -
674H HIS* 5.1 4.3 - - + -
702H ASN* 3.5 8.3 - - - +
703H PRO* 1.3 79.5 - - - +
705H CYS* 1.3 62.4 + - - +
707H PHE* 3.5 1.7 + - - +
708H HIS* 3.0 53.5 + - + +
166L SER* 5.6 2.9 - - - +
167L ILE* 5.4 4.7 - - + -
177L PHE* 3.5 32.5 - - + -
180L TYR* 3.2 33.2 - - + +
181L ARG* 4.2 20.2 - - + +
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Residues in contact with CYS 705 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669H SER* 5.8 0.7 - - - -
673H CYS* 3.5 23.3 - - - -
692H LEU* 3.7 10.7 - - - +
695H ALA* 3.4 31.4 - - + -
696H ILE* 3.2 31.9 - - + -
702H ASN* 3.1 27.2 + - + +
703H PRO 3.3 0.4 - - - -
704H LEU* 1.3 75.4 - - - +
706H LYS* 1.3 63.2 + - - +
708H HIS* 3.1 6.1 + - - +
709H ARG* 3.1 20.6 + - - +
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Residues in contact with LYS 706 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696H ILE* 3.7 46.2 - - + +
700H PRO* 3.4 21.3 + - - +
702H ASN 3.5 14.0 + - - +
703H PRO 3.3 3.4 + - - +
705H CYS* 1.3 78.5 - - - +
707H PHE* 1.3 62.8 + - - +
709H ARG* 3.4 5.6 + - - +
710H ALA* 3.3 18.9 + - - +
725H GLU* 4.5 22.3 - - + +
728H GLU* 4.5 22.1 + - + +
729H LEU* 4.0 13.4 - - + +
732H ILE* 3.4 33.4 - - + +
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Residues in contact with PHE 707 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703H PRO 3.1 14.8 + - - +
704H LEU 3.7 2.0 - - - +
706H LYS* 1.3 77.7 - - - +
708H HIS* 1.3 87.0 + + - +
710H ALA* 3.1 9.7 + - - +
711H SER* 3.0 24.8 + - - -
726H LEU* 4.9 4.7 - - + -
729H LEU* 3.4 28.6 - - + +
738H LEU* 3.5 48.7 - - + -
739H VAL* 4.6 9.2 - - + -
742H LEU* 3.6 30.7 - - + -
167L ILE* 5.1 4.7 - - + -
169L LYS* 4.8 6.3 - - + -
177L PHE* 3.6 23.8 - + + -
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Residues in contact with HIS 708 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673H CYS* 4.0 13.2 - - + -
674H HIS* 6.0 0.2 - - - -
677H VAL* 3.5 37.1 - - + +
692H LEU* 3.9 17.3 - - + -
704H LEU* 3.0 44.3 + - + +
705H CYS 3.1 7.8 + - - +
707H PHE* 1.3 87.8 - + - +
709H ARG* 1.3 66.4 + - - +
711H SER* 3.0 8.5 + - - -
712H VAL* 2.9 28.2 + - + +
167L ILE* 3.3 32.2 - - + +
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Residues in contact with ARG 709 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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689H LEU* 4.1 23.9 + - + +
692H LEU* 3.4 33.6 - - + +
693H ASN* 3.8 40.0 + - - +
696H ILE* 3.8 17.7 - - + +
705H CYS 3.1 9.1 + - - +
706H LYS 3.6 7.4 - - - +
707H PHE 3.3 0.2 - - - -
708H HIS* 1.3 76.8 - - - +
710H ALA* 1.3 61.2 + - - +
712H VAL* 3.4 2.3 + - - +
713H LEU* 3.0 47.1 + - - +
725H GLU* 3.1 35.3 + - - +
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Residues in contact with ALA 710 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706H LYS 3.3 8.0 + - - +
707H PHE* 3.1 12.2 + - - +
709H ARG* 1.3 78.0 - - - +
711H SER* 1.3 57.3 + - - +
713H LEU* 3.3 6.1 + - - +
714H PHE* 2.9 29.7 + - - +
722H ALA* 4.0 15.1 - - - +
725H GLU* 3.6 13.1 + - + -
726H LEU* 3.7 36.3 - - + +
729H LEU* 6.0 0.2 - - + -
742H LEU* 4.6 3.6 - - + +
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Residues in contact with SER 711 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680H HIS* 5.0 2.1 + - - -
707H PHE* 3.0 22.0 + - - -
708H HIS* 3.3 17.4 + - - -
710H ALA* 1.3 73.9 - - - +
712H VAL* 1.3 64.9 + - - +
714H PHE* 3.5 10.9 + - - +
715H ALA* 3.5 18.7 + - - +
742H LEU* 4.1 23.2 - - - +
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Residues in contact with VAL 712 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676H GLY 5.5 0.7 - - - +
677H VAL* 5.3 9.0 - - + -
680H HIS* 3.5 45.1 - - + +
685H SER* 4.4 3.8 - - - +
688H ALA* 4.7 2.5 - - + -
689H LEU* 3.1 35.4 - - + -
692H LEU* 3.9 15.5 - - + -
708H HIS* 2.9 20.4 + - + +
709H ARG 3.9 3.6 - - - +
711H SER* 1.3 76.2 - - - +
713H LEU* 1.3 62.1 + - - +
715H ALA* 3.3 7.1 + - - +
716H ASN* 3.3 22.4 + - - +
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Residues in contact with LEU 713 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689H LEU* 3.3 19.3 - - + -
709H ARG* 3.0 32.0 + - - +
710H ALA 3.7 3.8 - - - +
712H VAL* 1.3 75.6 - - - +
714H PHE* 1.3 63.3 + - - +
716H ASN* 3.2 7.9 + - + +
717H GLU 3.2 16.6 + - - -
718H LYS* 3.4 53.1 + - + +
721H SER* 4.2 21.5 - - - -
722H ALA* 4.3 14.1 - - + +
725H GLU* 3.6 25.6 - - + +
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Residues in contact with PHE 714 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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710H ALA 2.9 14.3 + - - +
711H SER* 3.5 15.3 - - - +
712H VAL 3.3 0.2 - - - -
713H LEU* 1.3 75.9 - - - +
715H ALA* 1.3 64.2 + - + +
717H GLU* 3.3 14.6 + - - +
719H TYR* 4.0 14.2 - + - -
722H ALA* 4.3 6.9 - - + +
742H LEU* 4.7 12.3 - - + -
745H LYS* 3.5 50.0 - - + -
746H VAL* 3.5 24.9 - - + -
749H LYS* 4.1 29.6 - - + -
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Residues in contact with ALA 715 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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680H HIS* 3.7 24.2 - - + +
711H SER 3.5 6.6 + - - +
712H VAL 3.3 10.6 + - - +
714H PHE* 1.3 78.0 - - + +
716H ASN* 1.3 60.2 + - - +
717H GLU* 3.2 17.2 + - - +
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Residues in contact with ASN 716 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685H SER* 4.0 20.1 + - - -
686H GLU* 4.2 10.6 + - - +
689H LEU* 3.5 26.1 - - - +
712H VAL* 3.3 20.6 + - - +
713H LEU* 3.2 14.4 + - + +
715H ALA* 1.3 77.5 - - - +
717H GLU* 1.3 62.9 + - - +
718H LYS* 3.1 37.6 + - - +
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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
------------------------------------------------------------
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