Contacts of the helix formed by residues 84 - 97 (chain D) in PDB entry 4UN7
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 84 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36D TYR 2.8 13.1 + - - +
38D VAL* 4.9 0.9 - - - +
65D VAL* 3.3 15.4 - - - +
67D SER* 3.2 19.8 + - - -
82D VAL* 3.3 5.3 + - - -
83D SER* 1.3 73.2 - - - +
85D LYS* 1.3 57.8 + - - +
86D LYS* 3.3 8.0 + - - +
87D LEU* 3.1 29.7 + - - +
88D TYR* 2.8 32.2 + - - +
5F C 3.8 8.8 + - - -
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Residues in contact with LYS 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D TYR* 3.5 36.3 + - + +
84D SER* 1.3 71.2 + - - +
86D LYS* 1.3 64.1 + - - +
88D TYR* 3.4 0.9 + - - +
89D TYR* 3.1 50.9 + - + -
4F G 2.5 36.5 + - - +
5F C 3.0 26.2 + - - +
25H G 3.9 37.4 + - + +
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Residues in contact with LYS 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D LEU* 2.8 32.9 + - + -
64D ASN* 4.3 6.4 + - - +
65D VAL* 3.8 20.2 - - + -
84D SER* 3.1 8.1 + - - +
85D LYS* 1.3 79.5 - - - +
87D LEU* 1.3 58.1 + - - +
89D TYR* 3.2 2.9 + - - +
90D TYR* 2.8 32.4 + - + +
5F C 4.7 1.6 + - - +
25H G 3.2 62.6 + - + +
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Residues in contact with LEU 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D VAL* 3.7 11.0 - - + -
56D MET* 3.9 22.4 - - - -
59D LEU* 4.4 8.3 - - + -
60D ILE* 4.7 9.4 - - + -
63D LEU* 3.7 28.7 - - + -
65D VAL* 4.3 12.6 - - + -
82D VAL* 3.8 30.5 - - + -
84D SER* 3.1 22.5 + - - +
86D LYS* 1.3 77.7 - - - +
88D TYR* 1.3 63.0 + - - +
90D TYR* 3.5 4.8 - - + +
91D PHE* 3.0 48.7 + - + -
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Residues in contact with TYR 88 (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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24D LEU* 3.6 20.2 + - + +
25D TYR 3.6 36.8 - - - -
26D LYS* 3.7 22.6 + - + +
36D TYR* 3.8 21.3 - + + -
37D ARG 3.8 11.2 - - - -
38D VAL* 3.7 12.9 - - + +
84D SER 2.8 18.6 + - - +
85D LYS 3.6 2.7 - - - +
87D LEU* 1.3 77.9 - - - +
89D TYR* 1.3 99.3 + + - +
91D PHE* 3.8 2.1 - - - +
92D ALA* 2.9 35.9 + - + +
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Residues in contact with TYR 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D LYS* 3.6 25.1 - - - +
36D TYR* 4.0 11.0 + + - -
85D LYS* 3.1 41.0 + - + +
86D LYS 4.1 0.7 - - - +
88D TYR* 1.3 93.4 - + - +
90D TYR* 1.3 68.2 + - - +
92D ALA* 4.3 5.8 - - + -
93D ASN* 2.9 33.3 + - - -
25H G 3.2 64.4 + + + +
1I C 3.2 42.7 + + - -
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Residues in contact with TYR 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D VAL* 4.2 7.6 + - - +
8D SER* 5.1 1.4 - - - -
11D SER* 2.4 37.5 + - - -
59D LEU* 3.9 12.5 - - + +
63D LEU* 3.9 42.0 - - + -
86D LYS* 2.8 20.9 + - + +
87D LEU* 3.5 9.4 - - + +
88D TYR 3.3 0.2 - - - -
89D TYR* 1.3 79.3 - - - +
91D PHE* 1.3 82.8 + + - +
93D ASN* 4.0 4.4 - - - +
94D MET* 3.2 26.9 + - + +
25H G 5.2 1.2 + - - -
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Residues in contact with PHE 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D SER 3.5 23.8 - - - -
14D LEU* 4.0 12.3 - - + -
15D LEU* 3.6 25.0 - - + +
18D ILE* 3.9 21.3 - - + -
24D LEU* 4.1 18.4 - - + -
38D VAL* 3.9 15.0 - - + -
56D MET* 4.3 3.1 - - + -
59D LEU* 3.4 27.4 - - + -
87D LEU* 3.0 48.7 + - + +
88D TYR 4.0 2.0 - - - +
90D TYR* 1.3 86.4 - + - +
92D ALA* 1.3 61.4 + - - +
94D MET* 3.4 8.7 + - - +
95D LEU* 2.9 28.9 + - - +
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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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24D LEU* 4.1 16.0 - - + +
88D TYR* 2.9 33.3 + - + +
89D TYR* 4.1 11.7 - - + +
91D PHE* 1.3 75.8 - - - +
93D ASN* 1.3 60.8 + - - +
95D LEU* 3.3 6.8 + - - +
96D GLU* 3.0 31.2 + - - +
1I C 6.0 0.2 - - - +
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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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89D TYR* 2.9 24.2 + - - +
90D TYR* 4.0 4.1 - - - +
92D ALA* 1.3 74.9 - - - +
94D MET* 1.3 64.7 + - - +
96D GLU* 3.1 28.1 + - - +
97D ARG* 3.2 19.7 + - - +
24H C 3.7 22.0 + - - +
25H G 3.0 23.4 + - - -
1I C 3.1 22.1 + - - -
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Residues in contact with MET 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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8D SER* 3.8 7.0 - - - +
11D SER* 3.7 26.9 - - - +
12D ALA* 3.6 29.6 - - + +
15D LEU* 4.1 11.9 - - + -
90D TYR* 3.2 22.7 + - + +
91D PHE* 3.6 12.1 - - - +
93D ASN* 1.3 78.5 - - - +
95D LEU* 1.3 61.0 + - - +
97D ARG* 3.4 11.0 - - - +
98D ILE 3.3 15.8 + - - -
101D PHE* 3.6 35.4 - - + -
105D GLU* 4.4 9.6 - - - +
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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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15D LEU* 4.1 16.5 - - + +
19D ILE* 3.9 32.1 - - + -
24D LEU* 4.9 8.5 - - + -
91D PHE 2.9 17.3 + - - +
92D ALA* 3.6 7.9 - - - +
93D ASN 3.2 0.2 - - - -
94D MET* 1.3 74.4 - - - +
96D GLU* 1.3 65.7 + - - +
98D ILE* 3.2 46.2 + - + +
134D LEU* 5.3 6.7 - - + -
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Residues in contact with GLU 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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92D ALA* 3.0 15.6 + - - +
93D ASN* 3.1 27.3 + - - +
95D LEU* 1.3 77.9 - - - +
97D ARG* 1.3 59.1 + - + +
98D ILE* 3.5 5.0 + - - +
99D ARG* 4.6 10.7 + - - +
1I C 4.4 17.8 + - - -
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Residues in contact with ARG 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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93D ASN 3.3 17.0 + - - +
94D MET* 3.4 11.2 - - + +
96D GLU* 1.3 79.0 - - + +
98D ILE* 1.3 62.2 + - - +
99D ARG* 3.3 3.4 - - - +
100D LEU* 3.2 49.6 + - + +
101D PHE* 3.7 9.3 - - + -
22H C 2.8 55.5 + - - +
23H G 4.7 13.0 + - - -
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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