Contacts of the helix formed by residues 615 - 624 (chain A) in PDB entry 1N54
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 ASP 615 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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580A ASP* 3.6 16.7 - - - +
583A LYS* 3.9 19.4 - - + +
609A ILE* 3.9 8.5 - - - -
614A VAL* 1.3 76.3 - - - +
616A CYS* 1.3 65.9 + - - +
617A ALA* 3.2 10.6 + - - +
618A ALA* 2.8 32.3 + - - +
619A VAL* 3.3 13.0 + - - +
705A GLU* 3.9 14.1 - - - +
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Residues in contact with CYS 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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609A ILE* 3.9 15.3 - - - +
615A ASP* 1.3 70.3 - - - +
617A ALA* 1.3 68.0 + - - +
619A VAL* 3.0 14.6 + - - +
620A ALA* 3.0 11.8 + - - +
644A THR* 3.8 28.4 - - + +
648A MET* 3.9 28.3 - - - -
705A GLU* 3.3 23.3 - - + +
709A LEU* 4.4 21.1 - - + +
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Residues in contact with ALA 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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580A ASP* 4.6 7.6 - - - +
615A ASP* 3.2 11.9 + - - +
616A CYS* 1.3 76.6 - - - +
618A ALA* 1.3 66.4 + - - +
620A ALA* 2.9 24.2 + - - +
621A ASN* 3.1 16.0 + - - +
705A GLU* 5.0 6.4 + - + +
708A ASN* 4.2 22.2 - - - +
709A LEU* 5.0 5.9 - - - +
712A VAL* 5.5 5.2 - - + -
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Residues in contact with ALA 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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580A ASP* 4.4 9.3 + - - +
583A LYS* 3.9 29.8 - - + -
584A LEU* 3.6 10.8 - - - +
587A LEU* 4.3 14.1 - - + -
614A VAL* 5.0 0.7 - - + -
615A ASP* 2.8 27.2 + - - +
617A ALA* 1.3 71.2 - - - +
619A VAL* 1.3 60.9 + - - +
620A ALA 2.8 6.6 + - - -
621A ASN* 3.0 5.9 + - - +
622A TRP* 2.9 21.1 + - - +
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Residues in contact with VAL 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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587A LEU* 4.2 10.5 - - + +
605A VAL* 3.6 21.8 - - + -
609A ILE* 3.5 31.2 - - + -
614A VAL* 4.8 2.9 - - + -
615A ASP 3.3 4.5 + - - +
616A CYS 3.0 7.9 + - - +
618A ALA* 1.3 76.2 - - - +
620A ALA* 1.3 51.2 + - - +
622A TRP* 3.7 22.3 - - + +
623A ILE* 2.7 49.0 + - + +
640A ILE* 4.2 5.6 - - + -
641A LEU* 5.0 3.6 - - + -
644A THR* 3.5 24.0 - - + +
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Residues in contact with ALA 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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616A CYS 3.0 10.1 + - - +
617A ALA* 2.9 14.5 + - - +
618A ALA 2.8 1.8 + - - -
619A VAL* 1.3 73.8 - - - +
621A ASN* 1.3 62.6 + - - +
622A TRP 2.9 4.3 - - - -
623A ILE* 3.0 14.9 + - - +
624A PHE* 3.1 22.7 + - + -
641A LEU* 5.0 7.2 - - + -
709A LEU* 4.3 15.5 - - + -
712A VAL* 3.8 23.6 - - + -
713A ILE* 4.8 7.6 - - + -
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Residues in contact with ASN 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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584A LEU* 3.9 19.2 - - + +
617A ALA* 3.1 16.6 + - - +
618A ALA* 3.0 7.6 + - - +
620A ALA* 1.3 79.2 - - - +
622A TRP* 1.3 60.3 + - - +
624A PHE 3.9 0.2 - - - -
625A SER* 3.3 20.1 + - - -
712A VAL* 4.3 14.5 - - - +
716A ARG* 2.9 47.5 + - - +
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Residues in contact with TRP 622 (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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584A LEU* 3.6 15.7 - - + +
587A LEU* 3.9 36.8 + - + -
588A ARG* 4.7 7.4 - - - +
590A MET* 4.7 2.9 - - + -
591A PHE* 4.2 18.7 - + + +
601A ILE* 3.9 25.1 - - + -
605A VAL* 4.3 11.0 - - + -
618A ALA 2.9 16.0 + - - +
619A VAL* 3.7 16.2 - - + +
620A ALA 2.9 0.2 - - - -
621A ASN* 1.3 75.4 - - - +
623A ILE* 1.3 89.1 + - + +
624A PHE 3.1 1.6 - - - -
625A SER* 2.5 31.4 + - - -
627A GLU* 5.5 3.3 - - + +
628A LEU* 2.8 42.8 - - + +
636A PHE* 5.6 4.7 - + - -
640A ILE* 4.1 23.6 - - + -
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Residues in contact with ILE 623 (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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619A VAL* 2.7 31.1 + - + +
620A ALA 3.0 6.4 + - - +
622A TRP* 1.3 103.2 - - + +
624A PHE* 1.3 67.3 + - + +
625A SER 3.3 1.8 + - - -
628A LEU* 3.5 12.9 - - + +
632A PHE* 3.3 20.6 - - + -
637A VAL* 3.7 43.6 - - + +
638A TRP* 4.8 4.7 - - + -
640A ILE* 4.5 0.9 - - + -
641A LEU* 4.0 34.5 - - + +
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Residues in contact with PHE 624 (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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620A ALA* 3.1 21.4 + - - +
621A ASN 3.6 3.8 - - - -
623A ILE* 1.3 83.4 - - + +
625A SER* 1.3 59.1 + - - +
632A PHE* 3.9 13.2 - + - -
638A TRP* 4.2 6.1 - + - -
641A LEU* 4.0 23.1 - - + -
712A VAL* 6.3 0.2 - - + -
713A ILE* 3.9 15.0 - - + -
716A ARG* 3.0 54.7 + - + +
717A PHE* 3.4 52.7 - + - -
720A ILE* 3.7 31.6 - - + +
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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