Contacts of the helix formed by residues 91 - 101 (chain D) in PDB entry 1IVH
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 GLY 91 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87D SER* 3.6 16.5 + - - -
90D SER* 1.3 71.1 + - - +
92D ALA* 1.3 65.7 - - - +
94D GLY* 3.2 1.6 + - - -
95D LEU 3.0 18.9 + - - -
216D MET* 3.3 22.2 - - - +
265D LEU* 4.9 7.0 - - - +
363D ARG* 5.3 3.2 - - - +
367D ASP* 3.3 21.8 + - - -
371D TYR* 4.8 0.7 + - - -
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Residues in contact with ALA 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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39D ILE* 4.2 9.4 - - + -
90D SER* 4.0 3.8 + - - +
91D GLY* 1.3 75.2 - - - +
93D VAL* 1.3 57.5 + - - +
95D LEU* 3.2 2.9 + - - +
96D SER* 3.1 23.1 + - - -
216D MET* 3.6 23.0 - - - +
217D ARG 3.1 29.4 - - - +
218D GLY* 4.0 3.8 - - - -
219D SER* 3.4 22.8 - - - +
367D ASP* 3.9 3.6 + - - +
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Residues in contact with VAL 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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32D LEU* 3.6 35.7 - - + -
39D ILE* 4.0 9.2 - - + -
45D PHE* 3.9 19.3 - - + -
51D PHE* 3.6 30.5 - - + -
52D TRP* 4.0 15.3 - - + -
86D ILE* 3.8 5.6 - - + -
90D SER* 3.6 11.3 + - - +
91D GLY 3.4 0.4 - - - -
92D ALA* 1.3 75.7 - - + +
94D GLY* 1.3 61.9 + - - +
96D SER* 3.7 6.6 - - - -
97D TYR* 2.9 27.5 + - + +
218D GLY 5.7 1.6 - - - +
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Residues in contact with GLY 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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83D MET* 3.3 17.2 - - - +
86D ILE* 3.6 19.0 - - - +
87D SER* 3.8 16.8 - - - -
90D SER 3.1 12.7 + - - -
91D GLY 3.2 4.2 + - - -
93D VAL* 1.3 76.3 - - - +
95D LEU* 1.3 58.4 + - - +
97D TYR* 3.2 2.9 + - - +
98D GLY 2.8 24.1 + - - -
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Residues in contact with LEU 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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83D MET* 4.6 2.0 - - - -
91D GLY 3.0 12.7 + - - +
92D ALA 3.2 9.4 + - - +
94D GLY* 1.3 72.1 - - - +
96D SER* 1.3 65.5 + - - +
98D GLY* 2.8 12.3 + - - -
99D ALA* 2.9 14.2 + - + +
168D THR* 4.2 19.3 - - + +
213D LYS* 5.3 0.4 - - - +
216D MET* 3.7 20.0 - - + -
219D SER* 3.7 16.4 - - - +
258D LEU* 4.9 13.2 - - + -
370D LEU* 3.4 34.1 - - + -
371D TYR* 4.2 18.7 + - + +
399D FAD 4.7 11.9 - - + +
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Residues in contact with SER 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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48D LEU* 5.1 5.6 - - - +
52D TRP* 3.8 16.2 - - - -
92D ALA 3.1 8.7 + - - -
93D VAL* 3.7 9.2 - - - -
94D GLY 3.4 0.2 - - - -
95D LEU* 1.3 77.2 - - - +
97D TYR* 1.3 62.3 + - - +
99D ALA 3.2 0.5 + - - -
100D HIS* 3.1 20.3 + - - +
168D THR* 4.1 5.6 - - - -
169D ASN* 3.1 34.1 + - - +
218D GLY 4.4 2.6 + - - -
219D SER* 3.0 25.9 + - - -
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Residues in contact with TYR 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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52D TRP* 3.8 13.9 - - + -
55D LEU* 4.0 13.0 - - + -
60D VAL* 2.6 39.3 + - + -
61D LEU* 4.2 10.5 - - + -
63D ILE* 3.9 1.7 - - - +
79D HIS* 3.2 28.5 + + - -
82D VAL* 3.7 16.1 - - + +
83D MET* 4.1 24.2 - - + -
86D ILE* 3.5 29.6 - - + -
93D VAL 2.9 19.4 + - - +
94D GLY 3.5 6.3 - - - +
95D LEU 3.2 0.2 - - - -
96D SER* 1.3 75.7 - - - +
98D GLY* 1.3 56.2 + - - +
100D HIS* 3.7 0.8 - - - +
101D SER* 2.6 58.4 + - - -
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Residues in contact with GLY 98 (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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79D HIS* 5.5 0.7 - - - -
83D MET* 4.4 6.1 - - - -
94D GLY 2.8 10.7 + - - -
95D LEU 2.8 7.8 + - - -
97D TYR* 1.3 79.8 - - - +
99D ALA* 1.3 65.0 + - - +
101D SER* 4.1 4.0 - - - -
102D ASN* 3.0 24.3 + - - +
103D LEU* 3.3 7.2 + - - +
257D VAL* 5.9 1.6 - - - -
258D LEU* 4.3 21.8 - - - -
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Residues in contact with ALA 99 (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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95D LEU* 2.9 7.5 + - + +
96D SER 3.6 7.0 - - - +
98D GLY* 1.3 72.6 - - - +
100D HIS* 1.3 58.6 + - - +
103D LEU* 3.0 30.7 + - + +
104D CYS* 2.9 29.3 + - - +
131D GLY 4.5 4.4 - - - +
132D ALA* 4.8 3.6 - - - -
133D LEU 5.5 0.2 - - - +
168D THR* 3.7 33.9 - - + +
169D ASN* 3.9 7.6 - - + +
258D LEU* 6.1 0.2 - - - +
399D FAD 5.0 0.4 - - - +
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Residues in contact with HIS 100 (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 TRP* 3.0 30.2 + + + +
61D LEU* 3.5 18.5 - - + +
96D SER 3.1 16.2 + - - +
97D TYR* 3.7 3.1 - - - +
99D ALA* 1.3 77.7 - - - +
101D SER* 1.3 61.3 + - - +
104D CYS* 3.3 3.6 - - - +
105D ILE* 2.9 47.7 + - + +
124D LEU* 2.8 31.1 + - + -
129D TYR 3.1 26.0 - - - -
130D ILE* 3.6 1.2 - - - +
131D GLY 3.2 28.0 + - - +
169D ASN* 3.9 5.8 + - - +
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Residues in contact with SER 101 (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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61D LEU 3.1 26.6 - - - +
64D THR* 4.4 3.5 + - - -
79D HIS* 2.8 36.9 + - - -
97D TYR* 2.6 42.8 + - - -
98D GLY* 4.1 1.0 + - - -
100D HIS* 1.3 77.6 - - - +
102D ASN* 1.3 58.6 + - - +
105D ILE* 3.6 9.9 - - - +
106D ASN* 3.5 15.6 + - - +
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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