Contacts of the helix formed by residues 83 - 94 (chain A) in PDB entry 7NG0
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 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A ILE* 3.8 6.9 - - - +
80A ILE* 3.9 6.1 - - - +
82A ALA* 1.3 73.1 - - - +
84A GLU* 1.3 67.0 + - - +
85A ARG 3.4 2.5 - - - -
86A ARG* 3.2 22.6 + - - +
87A TRP* 3.1 22.0 + - - +
121A ARG* 5.2 0.6 - - - +
301A SO4 3.2 22.0 + - - -
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Residues in contact with GLU 84 (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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38A PRO* 3.7 24.4 - - + +
39A ASN* 4.6 5.2 + - - +
42A GLN* 5.3 2.6 - - - +
43A PRO* 4.3 19.8 - - - +
44A ARG* 4.8 5.3 - - + +
47A PHE* 3.2 37.8 - - + -
80A ILE* 4.0 26.0 - - + +
83A GLY* 1.3 75.9 - - - +
85A ARG* 1.3 53.1 + - + +
87A TRP* 3.1 10.9 + - + +
88A ARG* 2.8 51.9 + - - +
301A SO4 3.2 5.4 + - - +
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Residues in contact with ARG 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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44A ARG* 4.1 29.6 - - - +
47A PHE* 4.7 8.3 - - + -
51A LYS* 4.2 32.1 + - - +
52A ILE* 4.1 29.0 - - + +
55A LEU* 3.5 37.0 - - + +
84A GLU* 1.3 73.6 - - - +
86A ARG* 1.3 52.7 + - - +
88A ARG* 3.2 1.4 + - - +
89A ALA* 2.8 37.4 + - - +
121A ARG* 4.6 3.8 - - - +
301A SO4 2.9 37.3 + - - +
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Residues in contact with ARG 86 (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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55A LEU* 4.2 13.9 - - + -
59A ILE* 4.5 10.8 - - + -
64A ILE* 5.6 7.9 - - + +
65A ILE 6.1 0.2 - - - +
66A GLN* 3.5 56.4 + - - +
67A PRO 4.0 9.8 + - - -
68A ILE* 3.7 14.7 - - + +
69A VAL* 4.7 1.6 - - - +
82A ALA* 3.4 18.0 + - - +
83A GLY* 3.2 32.8 + - - +
84A GLU 3.3 0.4 - - - -
85A ARG* 1.3 74.4 - - - +
87A TRP* 1.3 56.2 + - - +
89A ALA* 3.7 2.7 - - - +
90A VAL* 2.9 36.3 + - + +
98A ILE* 4.2 4.3 - - + -
301A SO4 3.4 20.6 + - - +
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Residues in contact with TRP 87 (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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33A VAL* 3.2 29.6 + - + +
36A ILE* 3.5 44.1 - - + +
38A PRO* 3.7 33.9 - - + -
68A ILE* 4.8 2.9 - - + -
80A ILE* 3.6 22.7 - - + -
83A GLY 3.1 13.3 + - - +
84A GLU* 3.3 13.0 - - - +
86A ARG* 1.3 72.5 - - - +
88A ARG* 1.3 93.2 + - + +
90A VAL* 3.1 10.4 - - - +
91A GLN* 3.0 54.1 + - - +
98A ILE* 4.0 8.4 - - + +
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Residues in contact with ARG 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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47A PHE* 3.8 49.2 - - - +
49A GLU* 3.8 18.6 + - - -
52A ILE* 4.1 19.0 - - + +
84A GLU* 2.8 36.3 + - - +
85A ARG 3.8 2.9 - - - +
87A TRP* 1.3 92.6 - - + +
89A ALA* 1.3 60.0 + - - +
91A GLN* 3.3 15.1 + - - +
92A LYS* 3.1 33.2 + - + +
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Residues in contact with ALA 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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52A ILE* 3.6 13.6 - - - +
55A LEU* 4.1 4.7 - - + -
56A ALA* 3.2 46.4 - - - +
59A ILE* 3.9 10.5 - - + -
85A ARG 2.8 21.7 + - - +
86A ARG 3.7 3.6 - - - +
88A ARG* 1.3 70.7 - - - +
90A VAL* 1.3 60.5 + - - +
92A LYS* 3.3 4.0 + - - +
93A LEU* 3.0 22.2 + - - +
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Residues in contact with VAL 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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33A VAL* 3.8 25.8 - - + -
59A ILE* 4.1 21.8 - - + -
64A ILE* 5.1 4.3 - - + -
86A ARG* 2.9 21.7 + - + +
87A TRP 3.1 18.6 - - - +
89A ALA* 1.3 72.1 - - - +
91A GLN* 1.3 60.3 - - - +
93A LEU* 3.1 8.4 + - - +
94A GLY 2.9 23.2 + - - -
95A TRP* 3.1 43.0 + - + -
98A ILE* 3.8 21.3 - - + -
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Residues in contact with GLN 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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33A VAL* 3.6 25.3 + - + +
34A LYS* 5.7 2.0 - - - +
87A TRP* 3.0 46.7 + - - +
88A ARG* 3.3 27.3 - - - +
89A ALA 3.2 0.2 - - - -
90A VAL* 1.3 77.6 - - - +
92A LYS* 1.3 62.5 + - + +
94A GLY* 3.1 15.5 + - - -
95A TRP 5.0 1.8 - - - +
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Residues in contact with LYS 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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49A GLU* 3.4 28.8 + - - +
52A ILE* 4.1 10.5 - - + -
53A ASP* 2.8 39.0 + - - +
56A ALA* 4.6 5.8 - - + -
88A ARG* 3.1 13.0 + - + +
89A ALA* 3.5 9.4 - - - +
91A GLN* 1.3 81.2 - - + +
93A LEU* 1.3 63.8 + - - +
94A GLY* 3.3 1.4 + - - -
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Residues in contact with LEU 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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56A ALA* 3.2 34.1 - - + +
57A LEU* 5.6 1.8 - - + -
59A ILE* 3.7 26.2 - - + -
60A ARG* 3.8 20.2 - - + +
89A ALA 3.0 13.2 + - - +
90A VAL* 3.1 12.3 + - - +
92A LYS* 1.3 76.2 - - - +
94A GLY* 1.3 59.6 + - - +
95A TRP* 3.8 30.9 + - + +
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Residues in contact with GLY 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 VAL 2.9 3.6 + - - -
91A GLN 3.1 13.3 + - - -
92A LYS 4.2 1.6 - - - -
93A LEU* 1.3 80.0 - - - +
95A TRP* 1.3 67.9 + - - +
96A THR* 3.6 9.9 + - - +
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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