Contacts of the helix formed by residues 688 - 700 (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 ILE 688 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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603C PHE* 3.7 30.5 - - + -
608C LEU* 4.4 10.1 - - + -
611C ALA* 3.7 34.1 - - + -
612C MET* 4.3 5.2 - - + +
615C HIS* 4.0 22.2 - - + +
640C THR* 4.5 10.1 - - + -
655C ILE* 4.7 15.9 - - + -
685C SER 5.0 1.6 - - - +
686C SER 3.6 1.7 + - - +
687C ASP* 1.3 73.5 + - - +
689C THR* 1.3 64.3 + - - +
690C ALA 3.5 1.3 - - - -
691C SER* 3.1 12.6 + - - -
692C VAL* 2.8 38.1 + - + +
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Residues in contact with THR 689 (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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53A GLN* 3.8 35.4 - - + +
615C HIS* 3.2 24.7 + - + +
687C ASP* 2.6 29.6 + - - -
688C ILE* 1.3 77.0 - - - +
690C ALA* 1.3 60.5 + - - +
692C VAL* 3.1 3.1 + - - +
693C ASN* 2.9 32.6 + - - +
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Residues in contact with ALA 690 (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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678C ILE* 4.5 16.0 - - + +
682C ALA* 3.7 32.3 - - + +
683C LEU* 3.6 10.7 - - + +
687C ASP 4.6 2.2 + - - +
688C ILE 3.5 0.2 - - - -
689C THR* 1.3 80.6 - - - +
691C SER* 1.3 62.2 + - - +
693C ASN* 3.4 7.0 + - - +
694C CYS* 3.1 25.5 + - - +
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Residues in contact with SER 691 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654C GLY* 4.7 3.1 - - - -
655C ILE* 4.4 22.8 - - - +
656C LEU* 4.6 6.2 + - - +
658C ILE* 3.8 12.5 - - - +
682C ALA 5.0 1.0 + - - -
683C LEU* 3.5 37.4 + - - +
687C ASP 5.3 0.4 + - - -
688C ILE* 3.1 15.0 + - - -
690C ALA* 1.3 79.1 - - - +
692C VAL* 1.3 59.9 + - - +
694C CYS 3.6 0.2 + - - -
695C ALA* 3.0 28.6 + - - +
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Residues in contact with VAL 692 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612C MET* 5.5 2.0 - - + -
615C HIS* 3.7 44.4 - - + +
617C LEU* 3.8 25.6 - - + -
656C LEU* 5.6 2.5 - - + -
688C ILE* 2.8 35.2 + - + +
689C THR 3.6 2.9 - - - +
691C SER* 1.3 75.5 - - - +
693C ASN* 1.3 69.8 + - - +
695C ALA* 3.2 5.9 + - - +
696C LYS* 2.9 39.1 + - + +
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Residues in contact with ASN 693 (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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31A ASN* 5.9 0.4 + - - -
49A LYS* 3.9 13.0 + - - +
50A TYR* 3.5 37.3 + - + -
53A GLN* 2.9 33.1 + - - -
398B TRP* 5.4 1.0 - - - -
615C HIS* 5.8 1.2 - - - -
689C THR* 2.9 23.6 + - - +
690C ALA* 3.8 6.9 - - - +
691C SER 3.4 0.2 - - - -
692C VAL* 1.3 83.5 - - - +
694C CYS* 1.3 62.3 + - - +
696C LYS* 3.4 8.1 + - - +
697C LYS* 3.4 17.7 + - - +
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Residues in contact with CYS 694 (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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658C ILE* 3.8 24.5 - - + -
663C TRP* 3.8 20.0 - - - -
676C CYS* 2.0 53.2 - - + -
678C ILE* 5.7 0.4 - - + -
683C LEU* 4.5 7.4 - - + -
690C ALA 3.1 16.6 + - - +
693C ASN* 1.3 74.2 - - - +
695C ALA* 1.3 66.3 + - - +
697C LYS* 3.0 4.9 + - - +
698C ILE* 2.9 27.1 + - - +
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Residues in contact with ALA 695 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617C LEU* 5.1 3.6 - - + -
628C TRP* 4.2 8.3 - - + -
656C LEU* 3.7 25.8 - - + -
658C ILE* 4.4 1.9 - - + +
691C SER 3.0 19.0 + - - +
692C VAL* 3.2 7.2 + - - +
694C CYS* 1.3 76.2 - - - +
696C LYS* 1.3 57.8 + - - +
698C ILE* 3.1 4.8 + - - +
699C VAL* 2.9 31.7 + - - +
708C TRP* 3.6 22.0 - - + -
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Residues in contact with LYS 696 (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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31A ASN* 3.0 12.3 + - - +
32A ASN* 2.9 24.7 - - - +
50A TYR* 3.5 35.2 - - + +
398B TRP* 4.4 0.9 - - - -
615C HIS 2.8 26.8 + - - -
616C GLY 3.3 16.7 + - - -
617C LEU* 3.8 11.4 - - + -
620C TYR* 3.4 32.3 - - + +
692C VAL* 2.9 30.7 + - + +
693C ASN* 3.7 4.4 - - - +
694C CYS 3.2 0.4 - - - -
695C ALA* 1.3 75.8 - - - +
697C LYS* 1.3 60.4 + - - +
699C VAL* 3.4 4.2 - - - +
700C SER* 2.8 29.9 + - - -
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Residues in contact with LYS 697 (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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332B ASP* 2.5 32.3 + - - -
333B TYR* 2.7 63.1 + - + +
398B TRP* 3.6 28.9 - - + -
399B GLU* 2.7 29.5 + - - +
663C TRP* 4.5 4.0 - - + -
675C LEU* 2.8 29.3 + - - +
676C CYS* 4.5 13.7 - - - -
693C ASN 3.4 7.5 + - - +
694C CYS 3.0 9.9 + - - +
696C LYS* 1.3 79.5 - - - +
698C ILE* 1.3 59.8 + - - +
700C SER* 3.2 6.8 + - - -
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Residues in contact with ILE 698 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B TYR* 3.8 6.1 - - - -
353B TYR* 4.3 2.2 + - - +
658C ILE* 4.0 24.2 - - + -
663C TRP* 3.4 55.0 - - + +
694C CYS* 2.9 19.8 + - - +
695C ALA 3.1 6.7 + - - +
697C LYS* 1.3 78.4 - - - +
699C VAL* 1.3 62.4 + - - +
700C SER 3.2 1.0 + - - -
701C ASP* 3.2 18.5 + - - +
704C GLY 4.3 3.5 - - - +
707C ALA* 3.7 28.5 - - + -
708C TRP* 3.8 20.6 - - + +
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Residues in contact with VAL 699 (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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358B TYR* 5.0 0.7 + - - -
620C TYR* 3.6 26.7 - - + -
621C ARG* 5.1 6.1 - - + +
623C TYR* 3.3 38.4 - - + -
628C TRP* 3.8 14.4 - - + -
695C ALA 2.9 18.5 + - - +
696C LYS* 3.4 11.9 - - - +
698C ILE* 1.3 69.3 - - - +
700C SER* 1.3 60.7 + - - +
701C ASP 3.0 19.1 + - - +
704C GLY* 3.4 12.7 - - - -
705C MET* 3.5 21.8 - - + +
708C TRP* 4.1 3.6 - - + -
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Residues in contact with SER 700 (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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96A TYR* 3.9 0.2 + - - -
333B TYR* 4.3 6.3 - - - -
350B TYR* 2.5 38.4 + - - -
358B TYR* 3.4 6.8 - - - -
398B TRP* 3.6 18.4 - - - -
620C TYR* 3.5 17.0 + - - -
621C ARG* 3.5 17.5 + - - +
696C LYS 2.8 21.4 + - - -
697C LYS 3.5 7.6 - - - -
698C ILE 3.2 1.4 - - - -
699C VAL* 1.3 75.3 - - - +
701C ASP* 1.3 60.7 + - - +
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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