Contacts of the helix formed by residues 79 - 89 (chain 1) in PDB entry 1NNI
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 SER 79 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81 GLY 2.8 26.4 + - - -
101 PRO* 4.3 2.9 - - - -
711 SER* 3.3 11.1 + - - -
721 PRO* 4.0 3.7 + - - -
741 TYR* 3.6 34.3 - - - -
781 MSE 1.3 81.3 - - - +
801 GLY* 1.3 65.7 + - - +
811 ALA 3.6 4.1 + - - -
821 LEU* 3.0 18.4 + - - +
831 LYS* 3.0 16.8 + - - +
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Residues in contact with GLY 80 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741 TYR* 4.7 4.6 - - - +
781 MSE 3.7 2.2 + - - -
791 SER* 1.3 72.2 - - - +
811 ALA* 1.3 57.1 + - - +
831 LYS* 3.8 6.0 - - - +
841 ASN* 2.9 33.7 + - - +
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Residues in contact with ALA 81 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81 GLY 4.1 3.1 - - - +
101 PRO* 3.9 33.7 - - + -
341 LEU* 3.5 17.7 - - + +
391 LEU* 5.8 0.2 - - - +
791 SER* 3.7 8.3 - - - +
801 GLY* 1.3 78.3 - - - +
821 LEU* 1.3 60.3 + - - +
841 ASN* 3.7 5.8 + - - +
851 ALA* 3.2 16.3 + - - +
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Residues in contact with LEU 82 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61 ILE* 4.5 16.2 - - + -
81 GLY* 4.1 3.1 - - - -
341 LEU* 3.5 15.2 - - + +
691 LEU* 4.1 29.2 - - + -
701 LEU 3.9 9.6 - - - +
711 SER* 3.6 27.6 - - - -
781 MSE 3.8 21.8 - - + -
791 SER* 3.0 20.1 + - - +
811 ALA* 1.3 73.9 - - - +
831 LYS* 1.3 66.3 + - - +
851 ALA* 3.2 5.3 - - + +
861 LEU* 3.0 34.9 + - + +
1181 MSE 4.7 3.1 - - - -
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Residues in contact with LYS 83 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781 MSE 4.1 25.5 - - + -
791 SER 3.0 16.3 + - - +
801 GLY* 3.8 7.6 - - - +
821 LEU* 1.3 73.9 - - - +
841 ASN* 1.3 67.2 + - - +
861 LEU* 3.1 11.1 + - + +
871 ASP* 2.8 53.3 + - - +
1171 ASN* 5.6 1.8 - - - +
1211 VAL* 4.0 26.7 - - + +
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Residues in contact with ASN 84 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391 LEU* 5.3 2.8 - - + +
401 PRO 3.4 2.8 - - - +
411 VAL* 2.9 43.3 - - - +
421 PHE* 3.0 22.6 + - - +
801 GLY 2.9 18.1 + - - +
811 ALA* 3.7 7.0 - - - +
831 LYS* 1.3 76.4 - - - +
851 ALA* 1.3 65.5 + - - +
871 ASP* 3.0 21.8 + - - +
881 PHE* 3.2 20.8 - - - -
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Residues in contact with ALA 85 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61 ILE* 6.3 0.4 - - + -
341 LEU* 4.3 12.6 - - + -
391 LEU* 4.1 28.0 - - + +
571 LEU* 3.9 16.0 - - + +
811 ALA 3.2 12.2 + - - +
821 LEU* 3.2 18.4 - - + +
841 ASN* 1.3 81.8 - - - +
861 LEU* 1.3 64.7 + - + +
881 PHE* 2.9 20.6 + - - +
891 LEU* 3.8 1.6 + - - +
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Residues in contact with LEU 86 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61 ILE* 6.1 1.6 - - + -
691 LEU* 4.9 5.6 - - + -
781 MSE 3.7 26.5 - - + -
821 LEU* 3.0 31.1 + - + +
831 LYS* 3.5 10.8 - - + +
851 ALA* 1.3 78.0 - - - +
871 ASP* 1.3 59.5 + - - +
891 LEU* 2.7 36.6 + - + +
941 PHE* 3.8 21.9 - - + -
1211 VAL* 4.1 16.2 - - + -
1221 MSE 3.2 36.8 - - + -
1251 VAL* 5.7 5.2 - - + +
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Residues in contact with ASP 87 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421 PHE* 3.9 36.7 - - + +
831 LYS* 2.8 52.4 + - - +
841 ASN* 3.0 16.9 + - - +
861 LEU* 1.3 74.4 - - - +
881 PHE* 1.3 59.9 + - - +
891 LEU 3.4 6.1 + - - +
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Residues in contact with PHE 88 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391 LEU* 4.3 17.7 - - + -
401 PRO* 3.4 26.7 - - + -
421 PHE* 3.7 25.8 - + + -
481 GLN* 3.4 30.3 - - + -
491 SER* 5.8 1.1 - - - -
541 VAL* 3.9 35.7 - - + -
571 LEU* 4.5 4.3 - - + -
581 LYS* 3.7 20.7 + - - -
841 ASN* 3.2 38.8 + - - -
851 ALA* 2.9 16.6 + - - +
871 ASP* 1.3 78.3 - - - +
891 LEU* 1.3 66.9 + - + +
931 GLN* 4.7 0.3 + - - -
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Residues in contact with LEU 89 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61 ILE* 6.3 0.2 - - + -
571 LEU* 3.8 23.1 - - + -
581 LYS* 3.6 31.6 - - + -
611 VAL* 3.8 29.6 - - + -
851 ALA 4.2 6.5 - - - +
861 LEU* 2.7 24.6 + - + +
871 ASP 3.5 6.9 - - - +
881 PHE* 1.3 85.8 - - + +
901 SER* 1.3 66.7 + - - +
931 GLN* 3.7 14.1 - - + +
941 PHE* 3.5 32.1 - - + -
1251 VAL* 5.3 2.0 - - - +
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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