Contacts of the helix formed by residues 691 - 707 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686B ASP* 2.9 13.2 + - - -
689B GLY 3.4 2.2 - - - -
690B LEU* 1.3 78.4 - - - +
692B HIS* 1.3 67.3 + - - -
693B GLU* 3.3 3.1 - - - -
694B LYS* 3.3 3.0 + - - -
695B LEU* 3.0 23.3 + - - +
823B PRO* 6.5 0.7 - - - -
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Residues in contact with HIS 692 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LYS* 5.8 5.2 - - - +
691B GLY* 1.3 71.0 - - - -
693B GLU* 1.3 79.7 + - - +
695B LEU* 3.3 6.2 + - - +
696B THR* 2.9 31.2 + - - -
723B ASP* 2.9 36.4 + - - -
812B GLY* 6.0 0.7 - - - -
813B SER* 3.3 27.0 + - - -
815B ARG 5.3 2.7 - - - -
816B LEU* 3.9 23.9 - - + +
823B PRO* 6.6 0.2 - - - -
825B MET* 3.4 29.6 - - + +
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Residues in contact with GLU 693 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691B GLY* 3.3 0.8 - - - -
692B HIS* 1.3 97.6 + - - +
694B LYS* 1.3 68.5 + - + +
696B THR* 3.1 8.6 + - - -
697B GLN* 3.0 38.4 + - - +
723B ASP* 4.1 9.7 - - - +
811B TYR 5.6 1.2 - - - +
812B GLY* 6.0 1.6 - - - -
57D TRP* 5.5 12.0 - - + -
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Residues in contact with LYS 694 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690B LEU* 3.7 46.0 - - + +
691B GLY 3.3 5.8 + - - +
692B HIS 3.3 0.2 - - - -
693B GLU* 1.3 79.5 - - + +
695B LEU* 1.3 66.0 + - - +
697B GLN* 3.3 11.9 + - - +
698B ALA* 3.0 23.2 + - - +
852B PRO* 5.8 0.7 - - - +
855B VAL* 5.3 0.3 - - - +
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Residues in contact with LEU 695 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684B LEU* 3.7 35.4 - - + +
686B ASP* 4.0 22.7 - - + +
690B LEU* 4.9 1.9 - - - +
691B GLY 3.0 16.6 + - - +
692B HIS* 3.9 6.3 - - - +
694B LYS* 1.3 76.4 - - - +
696B THR* 1.3 65.0 + - - +
698B ALA* 3.0 4.8 + - - +
699B ARG* 2.9 20.1 + - - +
823B PRO* 4.0 16.4 - - + +
824B SER* 3.9 16.2 - - - +
825B MET* 3.6 32.8 - - + -
855B VAL* 4.3 15.7 - - + -
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Residues in contact with THR 696 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692B HIS* 2.9 29.0 + - - -
693B GLU* 3.4 10.3 - - - -
695B LEU* 1.3 76.5 - - - +
697B GLN* 1.3 57.9 + - + +
699B ARG* 3.1 29.7 - - - +
700B ASN* 2.9 35.4 + - - +
722B GLU* 5.3 0.9 - - - +
723B ASP* 4.6 8.3 + - - +
825B MET* 3.1 23.1 - - + +
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Residues in contact with GLN 697 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693B GLU* 3.0 30.5 + - - +
694B LYS* 3.9 9.4 - - - +
696B THR* 1.3 75.4 - - + +
698B ALA* 1.3 58.8 + - - +
700B ASN* 3.1 12.1 + - + +
701B GLN* 2.8 30.4 + - - +
57D TRP* 6.2 2.8 - - - -
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Residues in contact with ALA 698 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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684B LEU* 4.0 3.1 - - + +
694B LYS 3.0 13.5 + - - +
695B LEU 3.4 8.3 - - - +
697B GLN* 1.3 75.0 - - - +
699B ARG* 1.3 63.2 + - - +
701B GLN* 3.2 9.6 + - - +
702B LEU* 3.0 23.0 + - - +
851B LEU* 4.0 4.8 - - + +
852B PRO* 4.0 20.8 - - + +
855B VAL* 3.9 37.0 - - + -
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Residues in contact with ARG 699 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684B LEU* 3.5 15.5 - - + +
695B LEU 2.9 11.3 + - - +
696B THR* 3.1 27.9 + - - +
698B ALA* 1.3 76.1 - - - +
700B ASN* 1.3 81.4 + - - +
702B LEU* 3.2 4.9 + - - +
703B LEU* 2.9 44.3 + - + +
718B PRO* 4.0 21.2 - - - +
720B GLY 5.6 1.6 + - - -
721B LEU 4.8 6.1 + - - -
722B GLU* 2.9 42.2 + - - -
825B MET* 3.8 32.8 - - + +
826B GLU 5.5 0.4 - - - -
827B ILE* 4.1 20.0 - - + -
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Residues in contact with ASN 700 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696B THR* 2.9 26.6 + - - +
697B GLN* 3.1 13.1 + - + +
699B ARG* 1.3 103.9 + - - +
701B GLN* 1.3 62.4 + - - +
703B LEU* 3.2 12.0 + - - +
704B ALA* 3.0 24.8 + - - +
722B GLU* 5.3 0.6 + - - -
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Residues in contact with GLN 701 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697B GLN 2.8 12.4 + - - +
698B ALA* 3.4 10.1 - - - +
700B ASN* 1.3 76.3 - - - +
702B LEU* 1.3 61.8 + - - +
704B ALA* 3.4 6.4 + - - +
705B GLU* 3.2 37.3 + - + +
850B LYS* 3.5 24.0 + - - +
851B LEU* 3.6 18.1 - - + +
852B PRO* 3.7 21.9 - - - +
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Residues in contact with LEU 702 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682B PHE* 3.7 32.5 - - + -
684B LEU* 4.0 9.9 - - + -
698B ALA 3.0 12.7 + - - +
699B ARG* 3.6 8.7 - - - +
701B GLN* 1.3 76.9 - - - +
703B LEU* 1.3 59.4 + - + +
705B GLU* 3.3 4.1 + - + -
706B ALA* 3.0 26.6 + - + +
827B ILE* 3.9 13.7 - - + -
844B MET* 3.7 20.2 - - + -
847B LEU* 3.5 35.2 - - + +
848B ALA* 3.8 12.1 - - + +
851B LEU* 3.9 13.0 - - + +
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Residues in contact with LEU 703 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699B ARG* 2.9 31.7 + - + +
700B ASN* 3.2 21.1 + - - +
702B LEU* 1.3 76.6 - - + +
704B ALA* 1.3 61.4 + - - +
706B ALA* 3.7 4.6 + - - +
707B ALA* 3.2 22.3 + - - +
716B VAL* 3.5 38.5 - - + +
717B ARG* 3.8 18.2 - - - +
718B PRO* 3.9 23.8 - - + -
827B ILE* 4.4 10.8 - - + -
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Residues in contact with ALA 704 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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700B ASN 3.0 12.5 + - - +
701B GLN* 3.6 11.2 - - - +
702B LEU 3.2 0.2 - - - -
703B LEU* 1.3 76.3 - - - +
705B GLU* 1.3 72.2 + - - +
707B ALA* 3.2 16.0 + - - +
708B LYS* 3.4 19.0 - - - +
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Residues in contact with GLU 705 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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701B GLN* 3.2 28.4 + - + +
702B LEU* 3.9 5.8 - - + +
704B ALA* 1.3 79.7 - - - +
706B ALA* 1.3 66.4 + - - +
707B ALA 3.0 2.0 - - - -
708B LYS* 2.9 47.5 + - - +
709B HIS* 3.3 17.9 + - + -
847B LEU* 3.9 26.5 - - + +
851B LEU* 6.1 1.8 - - + -
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Residues in contact with ALA 706 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702B LEU 3.0 16.7 + - - +
703B LEU* 3.9 3.6 - - - +
705B GLU* 1.3 77.1 - - - +
707B ALA* 1.3 59.2 + - - +
708B LYS 3.1 1.4 + - - -
709B HIS* 3.5 10.6 + - - +
710B PRO 4.5 0.2 - - - -
713B LEU* 3.8 31.5 - - + +
716B VAL* 3.5 38.7 - - + +
844B MET* 4.4 3.8 - - + -
847B LEU* 3.7 15.3 - - + +
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Residues in contact with ALA 707 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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703B LEU 3.2 14.0 + - - +
704B ALA* 3.4 14.1 - - - +
705B GLU 3.0 1.0 - - - -
706B ALA* 1.3 77.3 - - - +
708B LYS* 1.3 59.6 + - + +
709B HIS 3.4 0.4 - - - -
710B PRO* 3.4 20.7 - - - +
716B VAL* 4.5 7.4 - - + +
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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
------------------------------------------------------------
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