Contacts of the helix formed by residues 605 - 621 (chain A) in PDB entry 1NHX
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 PRO 605 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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491A GLY 3.5 19.7 - - - +
494A LEU* 3.9 16.2 - - + -
495A ALA* 3.7 22.4 - - + +
498A LEU* 3.6 23.6 - - + -
603A ASP 3.2 8.1 - - - +
604A LEU* 1.3 94.0 - - + +
606A CYS* 1.3 65.7 + - - +
607A GLU* 4.3 1.6 - - - +
608A ILE* 3.0 18.0 + - + +
609A GLU* 3.2 10.0 + - - +
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Residues in contact with CYS 606 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604A LEU 3.6 2.0 + - - -
605A PRO* 1.3 72.7 - - - +
607A GLU* 1.3 62.8 + - - +
609A GLU* 3.2 21.4 + - - +
610A ARG* 2.9 59.0 + - - +
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Residues in contact with GLU 607 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451A GLN* 3.5 30.6 + - + +
498A LEU* 3.5 44.6 - - + +
502A GLN* 4.6 12.5 + - - +
605A PRO* 3.2 1.7 - - - +
606A CYS* 1.3 83.5 - - - +
608A ILE* 1.3 57.0 + - - +
610A ARG* 3.5 29.3 + - - +
611A GLU* 3.1 32.5 + - - +
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Residues in contact with ILE 608 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451A GLN 4.7 1.6 - - - +
454A VAL* 3.9 28.3 - - + -
455A PHE* 4.1 26.5 - - + +
458A ALA* 4.9 3.8 - - + -
494A LEU* 4.3 12.6 - - + -
498A LEU* 4.1 18.2 - - + -
596A LEU* 4.1 26.0 - - + -
604A LEU* 4.1 14.8 - - + -
605A PRO* 3.0 26.3 + - + +
607A GLU* 1.3 74.3 - - - +
609A GLU* 1.3 65.9 + - - +
610A ARG 3.1 0.2 - - - -
611A GLU* 3.1 4.5 + - - +
612A ILE* 2.9 25.7 + - + +
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Residues in contact with GLU 609 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597A VAL* 6.1 2.0 - - + +
601A ASN 5.6 0.9 - - - +
604A LEU* 4.0 29.0 - - + +
605A PRO 3.2 11.7 + - - +
606A CYS* 3.4 25.3 - - - +
608A ILE* 1.3 74.9 - - - +
610A ARG* 1.3 63.6 + - + +
612A ILE* 3.4 12.2 + - + +
613A LEU* 3.2 22.7 + - - +
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Residues in contact with ARG 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606A CYS* 2.9 42.9 + - + +
607A GLU* 3.5 33.1 - - - +
609A GLU* 1.3 78.6 - - + +
611A GLU* 1.3 59.1 + - + +
613A LEU* 3.4 6.6 + - - +
614A ALA* 2.9 29.7 + - - +
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Residues in contact with GLU 611 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449A SER* 4.2 3.5 + - - -
451A GLN* 3.4 35.4 - - + +
452A HIS* 3.4 33.6 + - - +
455A PHE* 3.7 24.8 - - + -
607A GLU 3.1 16.3 + - - +
608A ILE* 3.1 8.1 + - - +
610A ARG* 1.3 75.7 - - - +
612A ILE* 1.3 65.5 + - - +
614A ALA* 3.9 10.1 - - - +
615A LEU* 3.0 25.1 + - - +
618A ARG* 4.9 5.2 + - - -
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Residues in contact with ILE 612 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455A PHE* 3.7 26.7 - - + -
589A VAL* 3.9 8.3 - - + +
592A ILE* 4.9 0.7 - - + -
593A GLU* 3.7 47.6 - - + +
596A LEU* 4.0 29.4 - - + -
597A VAL* 4.8 6.1 - - + -
604A LEU* 4.3 11.2 - - + -
608A ILE* 2.9 25.0 + - + +
609A GLU* 3.6 9.6 - - - +
611A GLU* 1.3 75.9 - - - +
613A LEU* 1.3 64.6 + - + +
615A LEU* 3.4 3.5 + - - +
616A LYS* 3.2 24.4 + - + +
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Residues in contact with LEU 613 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609A GLU 3.2 14.4 + - - +
610A ARG* 3.9 6.5 - - + +
612A ILE* 1.3 78.9 - - + +
614A ALA* 1.3 59.2 + - - +
616A LYS* 3.2 27.1 + - + +
617A GLN* 2.9 59.9 + - + +
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Residues in contact with ALA 614 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610A ARG 2.9 18.9 + - - +
611A GLU* 3.9 11.9 - - - +
613A LEU* 1.3 75.0 - - - +
615A LEU* 1.3 57.6 + - - +
617A GLN* 3.3 14.8 + - - +
618A ARG* 2.9 52.6 + - - +
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Residues in contact with LEU 615 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452A HIS* 5.5 1.1 - - - +
455A PHE* 3.6 32.1 - - + -
554A PRO 3.3 26.9 - - - +
555A ILE* 4.2 12.1 - - + -
585A TRP* 4.8 13.9 - - + -
589A VAL* 3.9 16.4 - - + -
592A ILE* 4.9 3.6 - - + -
611A GLU 3.0 18.2 + - - +
612A ILE 3.7 4.3 - - - +
614A ALA* 1.3 75.4 - - - +
616A LYS* 1.3 57.6 + - - +
618A ARG* 3.3 15.6 + - - +
619A ILE* 2.9 55.6 + - + +
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Residues in contact with LYS 616 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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589A VAL* 3.7 31.8 - - + +
590A GLU* 5.9 0.7 - - - -
593A GLU* 2.6 42.5 + - - +
612A ILE* 3.2 12.3 + - + +
613A LEU* 3.2 31.4 + - + +
615A LEU* 1.3 78.0 - - - +
617A GLN* 1.3 58.0 + - + +
619A ILE* 3.4 3.9 + - - +
620A SER* 3.0 29.7 + - - -
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Residues in contact with GLN 617 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613A LEU* 2.9 46.9 + - + +
614A ALA* 3.7 16.6 + - - +
615A LEU 3.2 0.2 - - - -
616A LYS* 1.3 73.5 - - + +
618A ARG* 1.3 64.3 + - + +
620A SER* 2.6 24.9 + - - +
621A GLN* 3.3 10.4 + - - +
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Residues in contact with ARG 618 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448A LEU* 3.7 25.5 - - - +
452A HIS* 3.9 24.4 + - - -
552A LEU* 6.1 1.8 - - - -
553A THR 5.0 1.6 - - - -
554A PRO* 2.6 53.3 + - + +
611A GLU* 4.9 5.5 + - - -
614A ALA* 2.9 47.3 + - + +
615A LEU* 3.6 24.6 - - - +
617A GLN* 1.3 76.2 - - + +
619A ILE* 1.3 61.2 + - - +
621A GLN* 3.4 14.2 + - - +
622A MET* 3.8 6.6 + - - +
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Residues in contact with ILE 619 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554A PRO* 4.2 9.2 - - + -
555A ILE* 5.6 0.9 - - + -
582A LYS* 3.8 17.3 - - + +
585A TRP* 3.4 37.2 - - + +
586A ASP* 3.4 33.2 - - - +
589A VAL* 3.9 11.4 - - + -
615A LEU* 2.9 46.6 + - + +
616A LYS* 3.8 4.9 - - - +
618A ARG* 1.3 72.0 - - - +
620A SER* 1.3 64.2 + - - +
621A GLN 3.1 2.5 - - - -
622A MET* 2.9 35.8 + - - +
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Residues in contact with SER 620 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582A LYS* 3.4 22.3 + - - +
586A ASP* 5.4 2.2 - - - -
616A LYS 3.0 13.5 + - - -
617A GLN* 2.6 26.2 + - - -
619A ILE* 1.3 78.4 - - - +
621A GLN* 1.3 62.8 + - - +
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Residues in contact with GLN 621 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617A GLN 3.3 6.6 + - - +
618A ARG* 3.9 10.8 - - - +
619A ILE 3.1 1.2 - - - -
620A SER* 1.3 85.5 + - - +
622A MET* 1.3 59.7 + - - +
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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