Contacts of the helix formed by residues 683 - 695 (chain C) in PDB entry 3ZNS
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 683 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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580C VAL* 4.4 3.6 - - + -
581C HIS* 3.2 15.2 + - - +
668C GLY 3.2 19.7 + - - +
669C HIS* 3.6 7.6 + - - -
671C ALA 3.6 12.0 + - - +
682C PHE* 1.3 67.8 - - - +
684C SER* 1.3 66.3 + - - +
685C VAL* 3.6 7.6 + - - +
686C ALA* 3.1 28.4 + - + +
687C ILE* 2.9 26.4 + - - +
713C GLY 3.5 5.9 - - - -
714C THR* 2.9 45.5 + - - +
717C THR* 4.8 0.4 + - - -
840C GLU* 5.1 0.2 - - - +
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Residues in contact with SER 684 (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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638C ALA 4.9 0.3 + - - -
641C ALA* 3.5 18.6 - - - +
642C ALA* 3.4 39.9 + - - +
645C VAL* 4.1 16.9 - - - +
664C VAL* 5.3 2.3 - - - +
666C PRO 4.8 3.8 + - - -
668C GLY* 4.3 7.6 + - - -
682C PHE 3.1 12.1 + - - -
683C ASN* 1.3 71.3 + - - +
685C VAL* 1.3 59.5 + - - +
687C ILE* 3.3 3.0 + - - +
688C ALA* 2.9 28.4 + - - +
838C ALA* 5.9 0.4 - - - -
840C GLU* 5.9 0.9 - - - -
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Residues in contact with VAL 685 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645C VAL* 4.4 8.3 - - + -
683C ASN* 3.3 7.0 + - - +
684C SER* 1.3 77.2 - - - +
686C ALA* 1.3 57.8 + - - +
688C ALA* 3.4 3.2 + - - +
689C CYS* 3.0 26.9 + - - +
703C ILE* 4.0 27.1 - - + -
714C THR* 5.2 2.7 - - + +
795C LEU* 3.6 28.2 - - + +
796C VAL 4.6 4.7 - - - +
797C SER* 3.6 20.6 - - - +
838C ALA* 3.7 29.8 - - + -
840C GLU* 3.8 8.2 + - - +
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Residues in contact with ALA 686 (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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580C VAL* 3.6 15.4 - - + +
683C ASN* 3.1 36.6 + - + +
685C VAL* 1.3 74.8 - - - +
687C ILE* 1.3 60.7 + - - +
689C CYS 3.4 0.2 + - - -
690C ARG* 2.9 27.5 + - - +
703C ILE* 5.1 0.2 - - - -
714C THR* 5.0 2.0 + - + -
717C THR* 4.4 4.9 - - + +
718C PHE* 3.4 36.1 - - + -
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Residues in contact with ILE 687 (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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572C ALA* 5.3 1.8 - - + -
576C GLU* 3.6 27.8 - - + +
577C LEU* 3.6 30.3 - - + -
579C SER* 4.4 0.7 - - - -
580C VAL* 3.4 24.9 - - + -
581C HIS* 4.3 6.1 - - + -
642C ALA* 3.7 19.1 - - + +
646C THR* 3.7 14.1 - - - +
682C PHE* 4.1 7.4 - - + -
683C ASN 2.9 22.8 + - - +
684C SER* 3.6 6.3 - - - +
686C ALA* 1.3 74.3 - - - +
688C ALA* 1.3 65.2 + - - +
690C ARG* 3.2 2.1 + - - +
691C GLN* 2.9 31.9 + - + +
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Residues in contact with ALA 688 (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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645C VAL* 3.8 17.3 - - + +
646C THR* 3.5 33.6 + - - +
649C ALA* 4.3 8.3 - - + -
684C SER 2.9 17.2 + - - +
685C VAL 3.6 5.2 - - - +
687C ILE* 1.3 77.0 - - - +
689C CYS* 1.3 59.8 + - - +
691C GLN* 3.5 1.0 + - - +
692C LEU* 3.0 32.7 + - - +
795C LEU* 4.3 6.7 - - + -
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Residues in contact with CYS 689 (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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685C VAL 3.0 17.7 + - - +
686C ALA 3.6 4.9 - - - +
687C ILE 3.2 0.2 - - - -
688C ALA* 1.3 77.0 - - - +
690C ARG* 1.3 62.4 + - - +
692C LEU* 3.3 5.8 + - - +
693C GLN* 3.3 21.5 + - - +
701C ILE* 3.3 39.4 - - - +
703C ILE* 4.4 4.3 - - + -
718C PHE* 3.6 15.0 - - + -
724C VAL* 3.7 28.3 - - - -
795C LEU* 3.5 13.6 - - + +
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Residues in contact with ARG 690 (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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579C SER* 3.5 40.7 + - - +
580C VAL* 4.1 5.8 - - + +
686C ALA 2.9 18.7 + - - +
687C ILE 3.6 4.3 - - - +
689C CYS* 1.3 75.9 - - - +
691C GLN* 1.3 58.8 + - - +
693C GLN* 3.2 24.3 + - - +
694C GLN* 3.0 47.6 + - - +
717C THR* 3.3 37.2 + - - +
718C PHE* 3.7 23.3 - - + +
721C ASP* 4.0 12.1 + - - +
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Residues in contact with GLN 691 (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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575C GLU 4.5 0.9 - - - +
576C GLU* 3.6 38.6 + - + +
579C SER* 3.2 29.8 + - - -
646C THR* 4.2 10.1 - - + -
650C PHE* 3.4 19.7 - - + -
687C ILE* 2.9 28.2 + - + +
688C ALA 4.0 2.2 - - - +
690C ARG* 1.3 73.0 - - - +
692C LEU* 1.3 59.0 + - - +
694C GLN* 3.9 16.4 + - - +
695C GLN* 3.0 42.6 + - - +
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Residues in contact with LEU 692 (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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649C ALA* 3.9 21.5 - - + -
650C PHE* 3.3 30.5 - - + -
653C ALA* 4.6 3.4 - - + -
688C ALA 3.0 25.1 + - - +
689C CYS* 3.5 10.3 - - - +
691C GLN* 1.3 77.4 - - - +
693C GLN* 1.3 59.5 + - - +
696C SER 3.2 1.7 + - - -
697C LYS* 2.7 46.4 + - + -
698C ALA* 3.3 10.2 + - + +
701C ILE* 3.8 23.1 - - + -
793C LEU* 3.9 32.8 - - + -
795C LEU* 4.7 2.0 - - + -
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Residues in contact with GLN 693 (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 CYS 3.3 10.5 + - - +
690C ARG* 3.2 37.9 + - - +
692C LEU* 1.3 77.4 - - - +
694C GLN* 1.3 64.2 + - + +
696C SER* 3.3 12.1 + - - -
698C ALA 3.7 12.4 - - - +
699C SER* 4.3 5.0 + - - +
701C ILE* 4.2 10.1 - - + -
718C PHE* 4.3 2.4 - - - -
721C ASP* 3.2 13.7 + - - +
723C SER* 2.7 30.9 + - - -
724C VAL* 3.3 17.6 - - - +
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Residues in contact with GLN 694 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579C SER* 3.7 26.6 + - - +
690C ARG* 3.0 33.7 + - - +
691C GLN* 3.9 22.1 + - - +
693C GLN* 1.3 78.3 - - + +
695C GLN* 1.3 65.7 + - + +
696C SER* 3.3 4.9 + - - -
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Residues in contact with GLN 695 (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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650C PHE* 3.7 27.9 - - + -
691C GLN* 3.0 27.4 + - - +
692C LEU 4.7 0.4 - - - +
694C GLN* 1.3 78.4 - - + +
696C SER* 1.3 71.6 + - - +
697C LYS* 3.2 3.1 + - - +
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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