Contacts of the helix formed by residues 624 - 637 (chain C) in PDB entry 1NBY
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 SER 624 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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617C LEU 4.2 0.2 - - - -
618C ASP* 4.2 3.8 - - - -
619C ASN* 3.9 7.8 + - - +
622C GLY 3.8 3.6 + - - -
623C TYR* 1.3 74.7 - - - +
625C LEU* 1.3 66.8 + - - +
626C GLY 3.1 3.6 + - - -
627C ASN* 3.1 32.1 + - - +
628C TRP* 3.6 3.5 - - - -
720C VAL* 3.7 16.8 - - - +
721C GLN* 5.7 4.0 - - - +
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Residues in contact with LEU 625 (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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609C ALA 3.3 20.9 - - - +
612C MET* 3.7 32.3 - - + -
613C LYS* 3.9 19.1 - - + +
617C LEU* 4.1 9.0 - - + -
618C ASP* 3.3 33.7 + - + +
623C TYR 3.8 0.6 + - - -
624C SER* 1.3 73.4 - - - +
626C GLY* 1.3 64.1 + - - +
628C TRP* 3.0 15.3 + - + +
629C VAL* 3.3 13.0 + - + +
724C ILE* 4.0 17.9 - - + -
729C LEU* 3.8 22.0 - - + -
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Residues in contact with GLY 626 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624C SER* 3.1 5.1 + - - -
625C LEU* 1.3 77.7 - - - +
627C ASN* 1.3 61.3 + - - +
629C VAL* 3.3 1.4 + - - +
630C CYS* 3.0 26.9 + - - +
720C VAL* 3.2 32.2 - - - +
721C GLN* 4.5 3.1 - - - +
723C TRP* 4.1 1.4 - - - +
724C ILE* 4.0 18.1 - - - +
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Residues in contact with ASN 627 (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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623C TYR* 4.0 16.7 - - + +
624C SER* 3.1 41.9 + - - +
626C GLY* 1.3 75.5 - - - +
628C TRP* 1.3 58.6 + - + +
630C CYS* 3.8 1.4 - - - +
631C ALA* 2.9 29.8 + - - +
705C MET* 3.6 20.9 - - - -
711C TRP* 3.0 32.9 + - - +
715C CYS 5.0 0.2 - - - +
716C LYS* 5.3 0.7 - - - -
720C VAL* 3.6 23.0 - - - +
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Residues in contact with TRP 628 (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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612C MET* 3.5 24.5 - - + +
617C LEU* 3.2 60.6 + - + +
620C TYR* 4.8 5.2 - + - +
623C TYR* 3.7 18.9 - + + +
624C SER 3.6 11.9 - - - -
625C LEU* 3.0 7.2 + - + +
627C ASN* 1.3 75.0 - - + +
629C VAL* 1.3 60.0 + - - +
631C ALA* 3.7 2.6 - - - +
632C ALA* 2.9 29.5 + - - +
656C LEU* 4.4 14.4 - - + +
695C ALA* 4.0 12.6 - - + -
699C VAL* 3.8 38.6 - - + -
705C MET* 3.6 34.3 - - + -
708C TRP* 3.8 21.8 - + - -
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Residues in contact with VAL 629 (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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605C ARG* 3.8 33.7 - - + +
608C LEU* 5.0 1.8 - - + -
609C ALA* 3.8 33.0 - - + +
612C MET* 4.1 11.2 - - - -
625C LEU* 3.3 15.3 + - + +
626C GLY 3.9 4.9 - - - +
628C TRP* 1.3 73.4 - - - +
630C CYS* 1.3 67.2 + - - +
632C ALA* 3.2 3.5 + - - -
633C LYS* 2.9 19.8 + - - +
638C PHE* 3.5 13.9 - - + -
723C TRP* 4.0 20.6 - - + +
724C ILE* 3.9 7.6 - - + -
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Residues in contact with CYS 630 (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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626C GLY 3.0 17.1 + - - +
627C ASN* 3.8 2.2 - - - +
629C VAL* 1.3 79.2 - - - +
631C ALA* 1.3 61.6 + - - +
633C LYS* 3.2 1.8 + - - +
634C PHE* 3.1 40.1 + - - -
714C ARG 4.0 2.0 - - - -
715C CYS* 2.4 47.6 - - + -
718C THR* 5.2 1.8 - - - -
720C VAL* 5.0 1.6 - - + -
723C TRP* 3.0 45.5 - - + +
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Residues in contact with ALA 631 (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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627C ASN 2.9 20.5 + - - +
628C TRP* 3.7 5.4 - - - +
630C CYS* 1.3 78.1 - - - +
632C ALA* 1.3 56.4 + - - +
634C PHE* 3.3 2.9 + - - +
635C GLU* 2.9 40.7 + - + +
656C LEU* 4.2 11.9 - - + -
705C MET* 4.1 17.0 - - + -
708C TRP* 5.3 4.3 - - + -
711C TRP* 4.2 15.7 - - + +
715C CYS* 3.7 8.0 - - - -
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Residues in contact with ALA 632 (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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608C LEU* 3.6 30.5 - - + -
612C MET* 4.1 7.4 - - + -
628C TRP 2.9 19.0 + - - +
629C VAL 3.6 2.7 - - - +
631C ALA* 1.3 76.2 - - - +
633C LYS* 1.3 63.3 + - - +
636C SER* 3.0 25.3 + - - -
637C ASN 3.3 5.2 + - - -
638C PHE* 3.5 3.7 + - + -
655C ILE* 3.7 21.8 - - + +
656C LEU* 4.0 4.4 - - + +
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Residues in contact with LYS 633 (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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629C VAL 2.9 9.0 + - - +
630C CYS 3.4 9.2 - - - +
632C ALA* 1.3 77.3 - - - +
634C PHE* 1.3 87.2 + - + +
637C ASN* 2.9 42.6 + - - +
638C PHE* 3.4 32.2 - - + -
723C TRP* 3.3 35.4 - - + -
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Residues in contact with PHE 634 (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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630C CYS* 3.1 42.2 + - - +
631C ALA 4.2 1.8 - - - +
633C LYS* 1.3 104.8 - - + +
635C GLU* 1.3 62.3 + - - +
637C ASN* 5.7 1.7 + - - -
710C ALA* 4.0 23.7 - - + +
714C ARG* 3.3 47.6 - - + -
715C CYS* 3.8 1.8 - - - -
723C TRP* 3.7 15.7 - + - -
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Residues in contact with GLU 635 (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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631C ALA* 2.9 26.5 + - - +
634C PHE* 1.3 80.1 - - - +
636C SER* 1.3 59.3 + - - +
637C ASN* 5.9 0.2 - - - -
642C ALA* 5.4 0.2 - - - +
655C ILE 3.9 11.4 - - - +
656C LEU* 4.2 5.8 - - + +
657C GLN* 3.3 43.7 - - + +
708C TRP* 3.7 36.2 - - + +
709C VAL* 4.3 3.9 + - - +
710C ALA* 3.0 33.1 + - + +
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Residues in contact with SER 636 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632C ALA 3.0 3.8 + - - -
635C GLU* 1.3 78.0 - - - +
637C ASN* 1.3 75.3 + - - +
638C PHE 3.3 4.5 + - - -
639C ASN* 3.1 41.9 + - - +
642C ALA* 3.7 13.9 - - - +
654C GLY 3.7 11.0 - - - -
655C ILE* 2.9 27.5 + - - +
657C GLN* 4.5 0.4 - - - -
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Residues in contact with ASN 637 (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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602C VAL* 3.9 12.6 - - - +
632C ALA 3.3 0.2 + - - -
633C LYS* 2.9 42.4 + - - +
634C PHE 5.7 1.6 + - - -
635C GLU 5.9 0.2 - - - -
636C SER* 1.3 80.7 - - - +
638C PHE* 1.3 75.9 + - - +
639C ASN* 3.3 2.2 + - + +
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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