Contacts of the helix formed by residues 617 - 623 (chain A) in PDB entry 3NC0
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 ASN 617 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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613A GLU* 3.0 26.3 + - - +
614A ILE 3.3 4.2 + - - +
615A LEU 2.9 0.8 - - - -
616A ASN* 1.3 95.7 + - - +
618A ILE* 1.3 70.0 + - - +
619A ASN 2.9 4.5 + - - -
620A THR* 2.9 40.9 + - - +
621A ILE* 3.2 16.1 + - + +
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Residues in contact with ILE 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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614A ILE* 3.1 17.5 + - + +
615A LEU* 3.6 36.9 + - + +
617A ASN* 1.3 75.8 - - - +
619A ASN* 1.3 62.4 + - - +
621A ILE* 3.3 6.4 + - - +
622A ILE* 3.1 50.4 + - + +
633A PHE* 4.4 18.6 - - + -
634A TYR* 3.7 34.8 - - + +
637A VAL* 5.5 2.9 - - + -
656A LYS 5.2 2.9 - - - +
657A TYR* 4.5 8.7 - - + +
660A LEU* 4.1 13.9 - - + -
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Residues in contact with ASN 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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617A ASN 3.1 1.0 - - - -
618A ILE* 1.3 79.5 - - - +
620A THR* 1.3 69.6 + - + +
622A ILE* 4.3 7.4 - - - +
623A CYS* 3.1 34.9 + - - +
660A LEU* 4.1 21.3 - - + +
126B VAL* 3.3 36.0 - - + +
127B GLY* 5.0 6.4 + - - +
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Residues in contact with THR 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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574A HIS* 2.9 23.2 + - - -
616A ASN 5.7 0.4 - - - +
617A ASN* 2.9 35.6 + - - +
619A ASN* 1.3 84.5 - - + +
621A ILE* 1.3 63.0 + - - +
623A CYS* 3.9 8.3 - - - -
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Residues in contact with ILE 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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570A PHE* 3.4 54.3 - - + +
573A MET* 3.8 36.1 - - - +
574A HIS* 3.1 23.9 + - + -
614A ILE* 4.4 10.8 - - - +
617A ASN* 3.2 25.0 + - + +
618A ILE 3.7 5.6 - - - +
619A ASN 3.1 0.4 - - - -
620A THR* 1.3 84.5 - - - +
622A ILE* 1.3 62.2 + - + +
623A CYS 3.4 0.4 - - - -
633A PHE* 4.0 16.6 - - + -
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Residues in contact with ILE 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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618A ILE* 3.1 38.6 + - + +
619A ASN* 4.2 7.6 - - - +
621A ILE* 1.3 77.3 - - + +
623A CYS* 1.3 65.5 + - - +
624A ASP 3.0 5.2 + - - -
625A LEU* 3.0 36.2 + - + +
630A VAL* 4.1 21.8 - - + +
633A PHE* 3.5 40.8 - - + -
634A TYR* 4.0 17.9 - - + +
660A LEU* 5.2 4.7 - - + -
128B LYS* 4.4 4.4 + - - +
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Residues in contact with CYS 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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574A HIS* 3.6 21.1 - - - -
619A ASN* 3.1 24.8 + - - +
620A THR* 3.9 8.3 - - - -
621A ILE 3.4 0.4 - - - -
622A ILE* 1.3 77.8 - - - +
624A ASP* 1.3 76.9 + - - +
625A LEU 3.5 0.2 - - - -
127B GLY 4.4 15.2 - - - +
128B LYS* 3.6 31.5 + - - +
129B ARG 5.2 0.5 + - - -
144B LYS* 5.7 0.9 - - - -
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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