Contacts of the helix formed by residues 84 - 99 (chain A) in PDB entry 2NR7
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A ALA* 4.3 1.3 - - - -
82A ILE* 3.4 9.7 - - - +
83A GLU* 1.3 76.7 - - - +
85A GLN* 1.3 63.8 + - - +
86A LYS* 3.6 11.1 + - - +
87A VAL* 3.3 30.0 + - - +
88A ALA* 3.0 18.7 + - - +
127A ASN* 4.6 1.4 + - - -
131A PRO* 3.7 28.8 - - - +
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Residues in contact with GLN 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MSE 4.7 0.7 - - - +
2A ALA* 3.6 10.9 - - + +
3A ASN* 2.8 50.5 + - - +
6A LEU* 3.7 28.1 - - + +
7A LEU 4.3 0.6 - - - +
74A TRP* 3.7 10.1 - - - -
83A GLU 3.8 4.0 + - - -
84A SER* 1.3 71.2 + - - +
86A LYS* 1.3 57.9 + - - +
88A ALA* 3.2 3.5 + - - +
89A ASN* 2.8 63.4 + - - +
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Residues in contact with LYS 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A SER* 3.6 9.2 + - - +
85A GLN* 1.3 78.0 - - - +
87A VAL* 1.3 65.6 + - + +
89A ASN* 3.5 11.3 - - - +
90A ILE 3.1 19.8 + - - -
131A PRO* 4.2 4.0 - - - -
132A ASP* 2.5 46.6 + - - +
135A PHE* 3.4 48.9 - - + +
136A GLU* 5.3 3.2 + - - -
189A ILE 6.0 1.1 - - - +
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Residues in contact with VAL 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ILE* 4.2 2.0 - - + -
84A SER* 3.3 26.7 + - - +
86A LYS* 1.3 79.4 - - + +
88A ALA* 1.3 63.9 + - - +
90A ILE* 3.3 6.5 + - - +
91A LEU* 3.1 43.1 + - + +
126A VAL* 3.8 21.5 - - + -
131A PRO* 3.5 27.6 - - + +
134A LEU* 3.8 14.8 - - + -
135A PHE* 4.1 14.4 - - + +
138A ILE* 4.3 4.0 - - + -
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Residues in contact with ALA 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ALA* 3.6 27.8 - - + -
74A TRP* 3.6 14.8 - - + -
79A ALA* 4.1 9.6 - - + -
82A ILE* 3.8 19.2 - - + +
84A SER 3.0 8.4 + - - +
85A GLN 3.6 7.2 - - - +
87A VAL* 1.3 76.0 - - - +
89A ASN* 1.3 64.7 + - - +
91A LEU* 4.7 0.9 - - - -
92A VAL* 2.9 30.0 + - - +
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Residues in contact with ASN 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LEU* 5.1 1.8 + - - +
7A LEU* 3.6 29.4 - - + +
74A TRP* 4.1 1.4 - - - -
85A GLN* 2.8 54.4 + - - +
86A LYS* 3.5 14.3 - - - +
87A VAL 3.2 0.2 - - - -
88A ALA* 1.3 71.3 - - - +
90A ILE* 1.3 59.0 + - + +
93A ASP* 3.0 33.3 + - - +
135A PHE* 5.7 0.7 - - + -
189A ILE* 3.7 15.3 + - + +
192A LEU* 3.4 32.8 - - - +
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Residues in contact with ILE 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A LYS 3.1 12.8 + - - +
87A VAL* 3.4 11.4 - - - +
89A ASN* 1.3 81.4 - - - +
91A LEU* 1.3 64.9 + - - +
94A TRP* 3.2 9.2 + - - +
135A PHE* 3.8 26.9 - - + +
138A ILE* 3.9 23.8 - - + -
139A PHE* 3.7 50.9 - - + +
142A ARG* 3.0 44.2 + - - +
186A LEU* 4.5 1.3 - - + -
189A ILE* 3.9 15.0 - - + -
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Residues in contact with LEU 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A TRP* 3.7 43.6 + - + +
82A ILE* 4.2 9.6 - - + -
87A VAL* 3.1 37.0 + - + +
88A ALA* 3.9 3.4 - - - +
90A ILE* 1.3 75.0 - - - +
92A VAL* 1.3 65.7 + - - +
94A TRP* 3.1 15.1 + - + +
95A VAL* 3.2 17.2 + - - +
106A PRO* 3.5 37.2 - - + -
110A LEU* 6.1 0.4 - - + -
126A VAL* 4.4 7.9 - - + -
138A ILE* 3.6 28.0 - - + -
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Residues in contact with VAL 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LEU* 3.7 24.0 - - + -
69A LEU* 4.3 5.4 - - + -
73A TYR* 3.8 10.3 - - + +
74A TRP* 3.6 52.5 - - + +
77A TRP* 4.0 17.5 - - + -
79A ALA* 3.9 13.2 - - + -
88A ALA* 2.9 20.4 + - - +
91A LEU* 1.3 73.8 - - - +
93A ASP* 1.3 58.1 + - - +
95A VAL* 3.1 6.4 + - - +
96A TRP* 2.9 25.1 + - - +
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Residues in contact with ASP 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LEU* 4.5 2.2 - - + +
10A TYR* 3.6 20.8 + - + -
11A ILE* 3.6 11.5 - - + +
37A THR* 4.6 1.1 + - - -
89A ASN 3.0 19.7 + - - +
92A VAL* 1.3 79.2 - - - +
94A TRP* 1.3 60.6 + - - +
96A TRP* 3.3 8.8 + - - +
97A GLY* 3.1 18.2 + - - -
142A ARG* 2.8 37.0 + - - +
185A ARG* 2.8 33.4 + - - -
186A LEU* 5.1 1.4 - - - +
189A ILE* 3.8 9.9 - - + +
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Residues in contact with TRP 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ILE 3.2 12.0 + - - +
91A LEU* 3.1 12.1 + - + +
93A ASP* 1.3 76.2 - - - +
95A VAL* 1.3 58.5 + - - +
97A GLY* 3.3 0.9 + - - -
98A SER* 2.8 51.0 + - - -
101A TYR 4.3 1.1 - - - -
102A GLY* 3.6 14.1 - - - +
105A ILE* 3.5 38.4 - - + -
106A PRO* 3.7 32.8 - - + -
109A ILE* 4.9 1.1 - - + -
138A ILE* 4.0 13.0 - - + -
141A ALA* 3.9 15.3 - - + -
142A ARG* 3.4 49.4 - - + +
145A PHE* 3.8 35.9 - - + -
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Residues in contact with VAL 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A TYR* 3.6 1.0 - - - -
73A TYR* 3.5 24.2 - - + +
76A ARG* 3.6 37.5 - - + +
77A TRP* 3.5 37.0 - - + +
91A LEU 3.2 2.0 + - - +
92A VAL* 3.1 8.5 + - - +
94A TRP* 1.3 74.4 - - - +
96A TRP* 1.3 63.2 + - - +
99A GLY* 2.8 34.4 + - - +
102A GLY 3.7 15.9 - - - -
103A ILE* 3.9 5.8 - - + -
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Residues in contact with TRP 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ILE* 3.6 29.8 - - + +
15A GLU* 2.9 23.6 + - + +
37A THR* 3.4 18.4 - - - -
38A TRP* 3.5 39.2 - + + +
39A LYS 3.1 21.5 + - - -
43A TYR* 4.0 2.4 - - - -
56A LEU* 3.5 34.8 - - + -
64A VAL* 5.0 5.4 - - + -
68A VAL* 4.0 21.1 - - + -
69A LEU* 3.8 23.6 - - + -
73A TYR* 3.6 31.5 - + + -
92A VAL 2.9 13.4 + - - +
93A ASP* 3.3 13.0 - - - +
95A VAL* 1.3 78.1 - - - +
97A GLY* 1.3 57.7 + - - +
185A ARG* 3.7 13.0 - - - +
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Residues in contact with GLY 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A THR* 3.3 24.5 - - - -
40A ARG 3.4 2.6 + - - -
41A VAL* 2.9 29.2 + - - -
43A TYR* 3.4 11.2 - - - +
93A ASP 3.1 9.8 + - - -
94A TRP 3.8 1.1 - - - -
96A TRP* 1.3 82.6 - - - +
98A SER* 1.3 61.7 + - - +
142A ARG* 5.9 2.5 - - - -
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Residues in contact with SER 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A VAL* 2.7 29.9 + - - +
43A TYR* 3.4 8.6 - - - +
44A ASP 3.1 16.5 + - - -
94A TRP* 2.8 38.0 + - - -
97A GLY* 1.3 73.8 - - - +
99A GLY* 1.3 64.6 + - - +
100A LYS 3.4 0.9 + - - -
101A TYR* 3.6 13.9 + - - -
102A GLY 4.8 0.2 - - - -
142A ARG* 5.5 1.0 + - - -
145A PHE* 3.3 19.8 - - - -
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Residues in contact with GLY 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A TYR* 3.2 13.8 - - - -
44A ASP 3.4 10.1 - - - -
76A ARG* 4.4 4.7 - - - -
95A VAL* 2.8 39.5 + - - +
98A SER* 1.3 76.5 - - - +
100A LYS* 1.3 58.6 + - - -
102A GLY* 2.9 22.7 + - - -
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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