Contacts of the helix formed by residues 708 - 715 (chain C) in PDB entry 1NDM
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 TRP 708 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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628C TRP* 3.8 25.4 - + - -
631C ALA* 5.2 3.6 - - + -
635C GLU* 3.3 24.9 - - + +
656C LEU* 2.9 44.1 + - + +
657C GLN 4.7 4.5 + - - -
658C ILE* 4.8 4.3 - - + +
695C ALA* 3.6 41.3 - - + -
698C ILE* 3.8 27.8 - - + +
699C VAL* 4.1 7.6 - - + -
704C GLY 4.5 0.2 - - - -
705C MET* 2.8 44.5 + - + +
706C ASN 4.0 2.2 - - - -
707C ALA* 1.3 80.9 - - + +
709C VAL* 1.3 65.8 + - - +
710C ALA 3.3 1.1 - - - -
711C TRP* 2.9 21.8 + - + +
712C ARG* 3.1 12.1 + - - +
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Residues in contact with VAL 709 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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635C GLU* 3.8 1.6 + - - -
707C ALA 3.6 6.0 + - - +
708C TRP* 1.3 70.2 - - - +
710C ALA* 1.3 63.4 + - - +
712C ARG* 3.1 38.4 + - - +
713C ASN* 3.1 39.0 + - - +
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Residues in contact with ALA 710 (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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634C PHE* 3.9 27.5 - - + +
635C GLU* 3.0 35.7 + - + +
709C VAL* 1.3 78.8 - - - +
711C TRP* 1.3 55.5 + - - +
713C ASN* 3.6 4.7 + - - +
714C ARG* 3.0 38.3 + - - +
715C CYS* 4.7 0.2 - - - -
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Residues in contact with TRP 711 (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* 4.2 15.3 - + - -
627C ASN* 3.1 44.9 + - - -
631C ALA* 3.9 11.7 - - + -
635C GLU* 3.8 1.6 + - - +
705C MET* 3.3 42.4 - - + -
706C ASN* 3.4 35.9 - - - -
708C TRP* 2.9 22.4 + - + +
710C ALA* 1.3 77.7 - - - +
712C ARG* 1.3 72.7 + - - +
715C CYS* 2.8 55.8 + - + +
716C LYS* 2.8 47.7 + - + -
717C GLY 5.3 0.4 - - - -
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Residues in contact with ARG 712 (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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706C ASN* 2.8 69.0 + - - +
707C ALA 4.7 0.8 - - - -
708C TRP 3.1 6.2 + - - +
709C VAL* 3.1 48.9 + - - +
711C TRP* 1.3 85.6 - - + +
713C ASN* 1.3 72.2 + - - +
716C LYS* 3.4 26.9 + - + +
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Residues in contact with ASN 713 (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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709C VAL* 3.1 33.4 + - - +
710C ALA* 4.2 4.5 - - - +
712C ARG* 1.3 92.1 - - - +
714C ARG* 1.3 69.5 + - + +
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Residues in contact with ARG 714 (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* 4.3 3.3 - - - -
634C PHE* 3.3 57.5 + - + +
710C ALA* 3.0 17.6 + - - +
713C ASN* 1.3 87.5 - - + +
715C CYS* 1.3 64.3 + - - +
716C LYS 5.2 0.4 - - - -
718C THR* 3.6 17.6 + - - +
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Residues in contact with CYS 715 (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* 5.0 0.4 - - - +
630C CYS* 2.0 66.2 - - + -
631C ALA* 3.6 5.2 - - - -
634C PHE* 3.7 8.7 - - - -
710C ALA 4.7 0.4 - - - -
711C TRP* 2.8 39.3 + - + +
714C ARG* 1.3 73.2 - - - +
716C LYS* 1.3 67.8 + - - +
717C GLY 3.2 0.7 + - - -
718C THR* 2.6 25.1 + - - -
720C VAL* 3.5 10.7 - - + +
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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