Contacts of the helix formed by residues 84 - 95 (chain A) in PDB entry 4I6N
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 ALA 84 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A TRP* 3.8 36.8 - - + -
79A GLN* 4.7 0.4 - - - -
81A ILE* 3.9 22.3 - - + +
82A GLN 3.0 2.2 + - - -
83A ASN* 1.3 77.5 - - - +
85A CYS* 1.3 64.0 + - - +
86A ALA 3.1 3.9 + - - -
87A SER* 3.1 6.1 + - - -
88A GLN* 2.8 36.9 + - - +
127A LEU* 4.8 3.4 - - + -
128A THR* 4.9 2.5 - - - +
137A HIS* 4.3 0.9 - - - -
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Residues in contact with CYS 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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79A GLN* 3.3 21.7 - - - +
82A GLN 3.3 2.0 + - - -
83A ASN 3.2 4.8 - - - -
84A ALA* 1.3 76.7 - - - +
86A ALA* 1.3 59.4 + - - +
88A GLN* 4.2 0.7 - - - -
89A ALA* 2.8 33.3 + - - +
161A HIS* 3.7 7.9 - - + +
162A PHE* 3.7 18.9 - - - +
75B GLY 3.6 2.9 - - - -
101B GVE 1.8 83.7 - - + +
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Residues in contact with ALA 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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9A ILE* 3.6 35.4 - - + -
16A PHE* 3.7 16.5 - - + -
19A MSE 4.5 3.4 - - + -
83A ASN 4.6 0.4 + - - -
84A ALA 3.1 1.4 + - - -
85A CYS* 1.3 81.1 - - - +
87A SER* 1.3 57.0 + - - +
89A ALA* 3.6 2.6 + - - +
90A LEU* 3.1 27.9 + - - +
137A HIS* 4.2 2.3 - - + +
162A PHE* 3.5 29.2 - - + -
75B GLY 4.8 1.3 - - - +
101B GVE 5.0 0.2 - - - -
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Residues in contact with SER 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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6A TRP* 3.9 13.2 - - - -
19A MSE 3.3 18.8 - - - +
23A PHE* 3.3 18.2 - - - -
84A ALA 3.1 6.0 + - - -
86A ALA* 1.3 75.2 - - - +
88A GLN* 1.3 62.4 + - - +
90A LEU* 3.7 2.6 - - - +
91A ILE* 2.8 36.3 + - - +
127A LEU* 4.8 2.0 - - - -
133A ILE* 4.4 6.5 - - - +
137A HIS* 2.9 31.4 + - - +
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Residues in contact with GLN 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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77A SER* 2.8 37.1 + - - +
78A GLN 3.1 24.0 + - - -
79A GLN* 3.2 38.3 - - + +
84A ALA* 2.8 27.1 + - - +
85A CYS 3.8 3.1 - - - +
87A SER* 1.3 79.9 - - - +
89A ALA* 1.3 56.8 + - - +
91A ILE* 4.0 0.3 - - - +
92A ASN* 2.9 38.4 + - - +
124A GLY* 3.5 9.5 - - - -
127A LEU* 4.0 21.7 - - + +
128A THR* 4.5 4.7 + - - -
177A GLY* 5.0 2.2 - - - -
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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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50A ILE* 4.9 5.8 - - + -
85A CYS 2.8 18.4 + - - +
86A ALA 3.8 4.0 - - - +
88A GLN* 1.3 75.8 - - - +
90A LEU* 1.3 63.3 + - - +
92A ASN* 3.7 5.2 - - - +
93A LEU* 3.1 14.0 + - - +
162A PHE* 3.8 30.7 - - + +
163A VAL* 4.2 4.9 - - - +
164A THR* 2.7 33.0 + - - +
175A LEU 5.2 2.5 - - - -
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Residues in contact with LEU 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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16A PHE* 4.2 14.8 - - + +
19A MSE 3.8 35.0 - - + -
20A ILE* 3.7 36.1 - - + -
23A PHE* 3.9 15.0 - - + -
50A ILE* 4.1 24.0 - - + -
86A ALA 3.1 13.8 + - - +
87A SER* 3.9 3.6 - - - +
89A ALA* 1.3 81.0 - - - +
91A ILE* 1.3 57.6 + - - +
93A LEU* 3.1 7.8 + - + +
94A LEU* 2.9 42.4 + - + +
164A THR* 4.6 0.7 - - - -
221A VAL* 4.7 4.5 - - + -
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Residues in contact with ILE 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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23A PHE* 3.9 25.1 - - + -
75A TYR* 5.3 2.5 - - + -
77A SER* 5.6 0.7 - - - +
87A SER 2.8 24.0 + - - +
90A LEU* 1.3 69.0 - - - +
92A ASN* 1.3 60.1 + - - +
94A LEU* 4.4 6.1 - - + +
95A LEU* 2.8 57.4 + - + +
108A LEU* 4.3 10.8 - - + -
111A PHE* 4.3 12.3 - - + -
127A LEU* 4.0 25.4 - - + -
133A ILE* 3.7 40.6 - - + -
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Residues in contact with ASN 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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75A TYR* 4.0 7.8 - - - -
76A PHE* 3.7 22.9 - - - -
77A SER* 2.8 52.9 + - - -
88A GLN* 2.9 27.4 + - - +
89A ALA* 3.7 7.8 - - - +
91A ILE* 1.3 75.7 - - - +
93A LEU* 1.4 58.7 + - - +
95A LEU* 3.9 0.7 + - - +
96A ASN* 2.7 31.8 + - - +
175A LEU* 3.4 24.1 + - + +
177A GLY* 4.8 4.8 - - - +
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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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47A HIS 4.3 11.7 - - - +
48A GLY* 3.9 14.6 - - - -
49A PHE 3.9 21.8 - - - +
50A ILE* 4.0 10.5 - - + -
89A ALA 3.1 9.4 + - - +
90A LEU* 3.1 10.5 + - + +
92A ASN* 1.4 73.8 - - - +
94A LEU* 1.3 73.2 + - + +
96A ASN* 3.1 17.7 + - - +
97A CYS* 3.7 20.7 + - - -
164A THR* 3.6 19.9 - - + +
166A VAL* 4.2 8.9 - - + +
221A VAL* 3.6 41.7 - - + -
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Residues in contact with LEU 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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20A ILE* 4.4 24.0 - - + -
23A PHE* 4.6 8.3 - - + -
25A CYS* 4.3 8.3 - - + -
28A LEU* 3.5 32.3 - - + -
90A LEU* 2.9 38.0 + - + +
91A ILE* 4.0 4.9 - - - +
93A LEU* 1.3 87.0 - - + +
95A LEU* 1.3 62.9 + - + +
96A ASN 3.0 0.4 - - - -
97A CYS* 3.1 28.8 + - - +
102A VAL* 5.4 0.2 - - + -
104A LEU* 3.5 22.6 - - + +
108A LEU* 3.8 23.1 - - + -
221A VAL* 5.0 0.2 - - + -
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Residues in contact with LEU 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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75A TYR* 3.5 49.9 - - + +
91A ILE* 2.8 29.0 + - + +
92A ASN 4.7 0.2 - - - +
93A LEU 3.2 0.4 - - - -
94A LEU* 1.3 80.8 - - + +
96A ASN* 1.3 58.6 + - - +
97A CYS 3.5 0.7 - - - -
104A LEU* 3.9 28.3 - - + -
108A LEU* 4.1 18.8 - - + +
111A PHE* 3.8 18.8 - - + -
112A LYS* 2.8 53.6 + - + -
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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