Contacts of the helix formed by residues 691 - 707 (chain C) in PDB entry 5NC5
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 GLY 691 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686C ASP* 2.9 14.7 + - - -
689C GLY 3.3 2.6 - - - -
690C LEU* 1.3 79.8 - - - +
692C HIS* 1.3 66.9 + - - -
693C GLU* 3.3 3.6 - - - -
694C LYS 3.2 3.9 + - - -
695C LEU* 3.0 23.0 + - - +
823C PRO* 6.4 0.9 - - - -
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Residues in contact with HIS 692 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691C GLY* 1.3 73.4 - - - -
693C GLU* 1.3 74.9 + - - +
695C LEU* 4.5 4.9 - - - +
696C THR* 2.7 40.9 + - - -
721C LEU 6.1 0.7 - - - -
723C ASP* 3.0 33.9 + - - -
812C GLY* 6.3 0.4 - - - -
813C SER* 3.5 26.7 + - - -
815C ARG 5.7 0.4 - - - -
816C LEU* 3.9 19.4 - - + +
825C MET* 3.7 27.6 - - + +
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Residues in contact with GLU 693 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691C GLY* 3.3 1.4 - - - -
692C HIS* 1.3 100.4 + - - +
694C LYS* 1.3 65.5 + - + +
696C THR* 3.2 7.6 + - - -
697C GLN* 3.0 38.9 + - - +
723C ASP* 4.8 5.4 - - - +
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Residues in contact with LYS 694 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690C LEU* 3.8 36.8 - - + +
691C GLY 3.2 6.6 + - - +
693C GLU* 1.3 79.8 - - + +
695C LEU* 1.3 60.0 + - - +
697C GLN* 3.2 34.8 + - - +
698C ALA* 2.9 28.8 + - - +
852C PRO* 5.7 1.2 - - - +
855C VAL* 5.5 0.5 - - - +
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Residues in contact with LEU 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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684C LEU* 3.6 28.9 - - + -
685C ILE 4.5 0.7 - - - +
686C ASP* 3.9 25.1 - - + +
690C LEU* 5.1 4.4 - - + +
691C GLY 3.0 17.4 + - - +
692C HIS* 4.0 5.8 - - - +
694C LYS* 1.3 76.7 - - - +
696C THR* 1.3 62.3 + - - +
698C ALA* 3.3 2.4 + - + -
699C ARG* 3.0 21.8 + - - +
823C PRO* 4.1 10.3 - - + +
824C SER* 3.9 26.0 - - - +
825C MET* 3.8 33.2 - - + +
855C VAL* 4.4 14.4 - - + -
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Residues in contact with THR 696 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692C HIS* 2.7 31.3 + - - -
693C GLU* 3.3 11.3 - - - -
695C LEU* 1.3 77.6 - - - +
697C GLN* 1.3 62.8 + - + +
699C ARG* 3.2 29.5 + - - +
700C ASN* 3.1 29.2 + - - +
722C GLU* 4.8 4.3 - - - +
723C ASP* 4.7 8.2 + - - +
825C MET* 3.7 20.1 - - - +
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Residues in contact with GLN 697 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693C GLU* 3.0 26.3 + - - +
694C LYS* 3.2 35.2 + - - +
696C THR* 1.3 74.8 - - + +
698C ALA* 1.3 64.2 + - - +
700C ASN* 3.1 12.3 + - - +
701C GLN* 2.9 23.4 + - - +
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Residues in contact with ALA 698 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684C LEU* 4.1 3.5 - - + +
694C LYS 2.9 16.5 + - - +
695C LEU* 3.6 6.7 - - - +
697C GLN* 1.3 77.4 - - - +
699C ARG* 1.3 62.3 + - - +
701C GLN* 3.3 9.2 + - - +
702C LEU* 3.0 23.0 + - - +
851C LEU* 4.2 6.2 - - + +
852C PRO* 4.4 17.3 - - + -
855C VAL* 4.1 34.8 - - + -
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Residues in contact with ARG 699 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684C LEU* 3.6 14.0 - - + +
695C LEU 3.0 12.9 + - - +
696C THR* 3.2 20.7 + - - +
698C ALA* 1.3 74.3 - - - +
700C ASN* 1.3 89.9 + - - +
702C LEU* 3.1 5.9 + - - +
703C LEU* 2.8 45.8 + - + +
718C PRO* 3.9 25.3 - - - +
720C GLY 6.2 0.2 - - - -
721C LEU 4.6 6.9 + - - -
722C GLU* 2.7 42.1 + - - -
825C MET* 3.9 30.4 - - + +
827C ILE* 3.7 20.0 - - + -
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Residues in contact with ASN 700 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696C THR* 3.1 23.0 + - - +
697C GLN* 3.1 12.3 + - - +
699C ARG* 1.3 108.7 + - - +
701C GLN* 1.3 57.7 + - - +
703C LEU* 3.8 10.8 - - - +
704C ALA* 2.9 32.1 + - - +
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Residues in contact with GLN 701 (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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697C GLN 2.9 12.5 + - - +
698C ALA* 3.4 11.2 - - - +
699C ARG 3.2 0.2 - - - -
700C ASN* 1.3 75.8 - - - +
702C LEU* 1.3 63.8 + - - +
704C ALA* 3.4 5.8 + - - +
705C GLU* 3.2 28.4 + - + +
850C LYS* 3.5 23.2 + - - +
851C LEU* 3.9 11.2 - - + +
852C PRO* 3.7 23.3 - - - +
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Residues in contact with LEU 702 (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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682C PHE* 3.6 32.5 - - + -
684C LEU* 3.7 14.8 - - + -
698C ALA 3.0 13.8 + - - +
699C ARG* 3.5 7.2 - - - +
701C GLN* 1.3 74.6 - - - +
703C LEU* 1.3 59.8 + - + +
705C GLU* 3.0 9.0 + - - +
706C ALA* 2.8 28.3 + - + +
827C ILE* 4.1 15.0 - - + -
844C MET* 4.2 18.6 - - + +
847C LEU* 3.6 36.1 - - + +
848C ALA* 4.0 12.3 - - - +
851C LEU* 4.0 12.1 - - + +
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Residues in contact with LEU 703 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699C ARG* 2.8 49.7 + - + +
700C ASN* 3.8 10.8 - - - +
702C LEU* 1.3 74.0 - - + +
704C ALA* 1.3 57.7 + - - +
706C ALA* 3.5 7.2 + - - +
707C ALA* 3.1 26.3 + - - +
716C VAL* 3.6 38.0 - - + +
717C ARG* 4.2 7.2 - - - +
718C PRO* 3.8 18.6 - - + -
827C ILE* 4.2 20.2 - - + -
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Residues in contact with ALA 704 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700C ASN 2.9 17.5 + - - +
701C GLN* 3.7 6.7 - - - +
703C LEU* 1.3 74.0 - - - +
705C GLU* 1.3 65.6 + - + +
707C ALA* 3.2 19.2 + - - +
708C LYS* 3.4 19.6 - - - +
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Residues in contact with GLU 705 (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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701C GLN* 3.2 17.8 + - + +
702C LEU* 3.0 11.5 + - - +
704C ALA* 1.3 78.0 - - - +
706C ALA* 1.3 64.4 + - - +
708C LYS* 2.8 41.8 + - - +
709C HIS* 3.1 29.1 + - - -
847C LEU* 3.7 31.2 - - + +
851C LEU* 6.4 1.1 - - + -
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Residues in contact with ALA 706 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702C LEU* 2.8 14.5 + - + +
703C LEU* 3.6 10.8 - - - +
705C GLU* 1.3 77.5 - - - +
707C ALA* 1.3 56.6 + - - +
708C LYS 3.1 0.4 - - - -
709C HIS* 3.1 25.7 + - - +
713C LEU* 3.9 28.1 - - + +
716C VAL* 4.1 25.1 - - + +
844C MET* 4.8 5.2 - - - -
847C LEU* 3.9 14.0 - - + +
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Residues in contact with ALA 707 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703C LEU 3.1 13.7 + - - +
704C ALA* 3.3 15.7 - - - +
705C GLU 3.1 0.4 - - - -
706C ALA* 1.3 76.3 - - - +
708C LYS* 1.3 57.6 + - + +
709C HIS 3.3 1.0 + - - -
710C PRO* 3.7 14.9 - - - +
716C VAL* 6.4 0.4 - - - -
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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