Contacts of the helix formed by residues 88 - 97 (chain D) in PDB entry 1NQ3
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 88 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51D VAL* 3.8 44.6 - - + +
83D LEU* 4.6 4.0 - - + -
85D ASP* 2.9 34.0 + - - +
87D ASN* 1.3 79.5 - - - +
89D PHE* 1.3 64.1 + - - +
90D SER 3.4 1.1 - - - -
91D ALA* 3.2 9.1 + - - +
92D VAL* 3.0 25.3 + - + +
120D ARG* 4.6 11.3 + - - +
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Residues in contact with PHE 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D VAL* 5.5 4.9 - - + -
83D LEU* 3.8 20.5 - - + +
86D ILE* 3.1 22.4 + - + +
87D ASN 3.1 1.8 - - - -
88D ASP* 1.3 77.5 - - - +
90D SER* 1.3 58.5 + - - +
92D VAL* 3.3 5.4 + - + +
93D ASN* 2.8 34.7 + - + +
107D ARG* 3.8 33.9 - - - -
109D ALA* 3.7 27.8 - - + -
116E PRO* 4.6 24.0 - - + -
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Residues in contact with SER 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D ASN 4.5 4.7 + - - -
88D ASP 3.4 0.8 - - - -
89D PHE* 1.3 77.5 - - - +
91D ALA* 1.3 57.3 + - - +
93D ASN* 3.2 8.6 + - - +
94D ASP* 2.9 36.0 + - - +
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Residues in contact with ALA 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D VAL* 4.9 7.4 - - + -
52D VAL* 4.1 23.7 - - + +
87D ASN 5.3 0.4 + - - +
88D ASP* 3.2 14.8 + - - +
90D SER* 1.3 78.5 - - - +
92D VAL* 1.3 62.7 + - - +
94D ASP* 3.3 18.2 + - - +
95D VAL* 3.4 17.3 + - - +
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Residues in contact with VAL 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D VAL* 3.6 30.1 - - + -
52D VAL* 6.1 0.4 - - - +
55D ALA* 4.3 20.4 - - + -
59D LEU* 6.2 0.7 - - + -
81D VAL* 4.1 25.1 - - + -
83D LEU* 3.8 17.0 - - + -
88D ASP 3.0 17.2 + - - +
89D PHE* 3.8 5.2 - - + +
91D ALA* 1.3 73.6 - - - +
93D ASN* 1.3 62.2 + - - +
95D VAL* 3.0 9.4 + - - +
96D TYR* 2.8 30.8 + - + +
121D VAL* 4.5 6.5 - - + -
123D ILE* 5.1 6.7 - - + -
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Residues in contact with ASN 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B GLN* 3.8 27.9 + - - +
89D PHE* 2.8 27.2 + - + +
90D SER* 3.2 9.3 + - - +
92D VAL* 1.3 78.8 - - - +
94D ASP* 1.3 62.8 + - - +
96D TYR* 3.4 5.5 - - - +
97D LYS* 2.9 29.3 + - - +
107D ARG* 2.9 33.6 + - - +
19E GLY* 5.4 0.6 - - - -
20E PRO* 3.3 14.8 - - - +
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Residues in contact with ASP 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B LYS* 6.1 0.5 - - - +
98B GLN* 5.6 0.2 + - - -
90D SER* 2.9 20.2 + - - +
91D ALA* 3.5 13.6 - - - +
92D VAL 3.2 0.2 - - - -
93D ASN* 1.3 81.5 + - - +
95D VAL* 1.3 60.5 + - + +
97D LYS* 3.4 40.1 + - - +
98D GLN* 3.3 17.7 - - - +
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Residues in contact with VAL 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D VAL* 4.1 31.0 - - + +
55D ALA* 4.1 9.0 - - + -
56D LYS* 3.7 44.6 - - + +
59D LEU* 4.0 12.8 - - + -
91D ALA 3.6 12.8 - - - +
92D VAL* 3.0 8.3 + - - +
94D ASP* 1.3 76.8 - - + +
96D TYR* 1.3 68.5 + - - +
98D GLN* 3.1 22.3 + - - +
99D TYR* 3.2 20.0 - - + -
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Residues in contact with TYR 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D LEU* 3.7 27.5 - - + +
79D ALA* 3.4 26.6 - - + +
81D VAL* 4.2 25.1 - - + -
92D VAL* 2.8 19.4 + - + +
93D ASN* 3.4 9.2 - - - +
95D VAL* 1.3 76.8 - - - +
97D LYS* 1.3 63.4 + - - +
99D TYR* 3.0 15.1 + - - +
100D PHE* 3.3 48.0 - + - -
105D PRO* 4.4 10.3 - - + +
107D ARG* 3.8 33.6 - - - +
123D ILE* 4.7 6.3 - - + -
20E PRO* 3.6 28.0 - - + -
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Residues in contact with LYS 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B LYS* 2.9 29.1 + - - +
98B GLN* 3.3 50.5 - - + +
100B PHE 3.4 7.7 + - - -
101B GLN* 3.3 21.9 - - - +
93D ASN 2.9 9.5 + - - +
94D ASP* 3.4 42.3 + - - +
96D TYR* 1.3 75.1 - - - +
98D GLN* 1.3 61.8 + - + +
99D TYR 3.1 0.4 - - - -
100D PHE* 2.8 24.6 - - - +
101D GLN* 5.8 0.3 - - - +
20E PRO* 4.1 17.5 - - + -
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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