Contacts of the helix formed by residues 85 - 101 (chain A) in PDB entry 4BKR
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 THR 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A ALA* 4.0 1.8 - - - -
75A GLU* 2.6 31.2 + - - +
76A ARG* 3.0 56.3 + - + +
84A GLY* 1.3 76.1 - - - -
86A SER* 1.3 68.0 + - - +
87A GLY 4.2 0.2 - - - -
88A TRP* 3.1 11.6 + - - +
89A TYR* 3.3 11.4 + - - -
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Residues in contact with SER 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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15A ALA* 3.7 14.2 - - - +
20A CYS* 4.0 12.8 - - - -
51A THR* 3.9 11.8 - - - +
85A THR* 1.3 72.7 - - - +
87A GLY* 1.3 54.4 + - - +
89A TYR* 3.1 3.2 + - - +
90A ASN* 2.7 42.3 + - - +
277A GLN* 4.9 4.3 + - - -
373A LEU* 3.4 26.6 + - - +
374A PHE* 4.1 22.8 - - - -
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Residues in contact with GLY 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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50A SER* 3.5 8.6 - - - -
51A THR* 3.4 25.6 - - - +
75A GLU* 3.6 21.3 + - - -
85A THR 3.2 1.0 - - - -
86A SER* 1.3 82.2 + - - +
88A TRP* 1.3 61.0 + - - +
91A SER* 2.9 31.0 + - - -
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Residues in contact with TRP 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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73A PHE* 4.5 3.4 - + - -
75A GLU* 3.8 17.5 - - + +
76A ARG 3.5 15.9 - - - +
77A PRO* 3.6 45.0 - - + +
78A GLY 4.1 5.1 - - - +
84A GLY 4.9 0.2 - - - -
85A THR* 3.1 18.3 + - - +
87A GLY* 1.3 75.9 - - - +
89A TYR* 1.3 75.0 + + - +
91A SER* 3.2 4.4 + - - -
92A ALA* 2.9 25.6 + - + +
109A ASN* 3.9 16.8 - - - -
391A VAL* 2.7 28.0 + - + -
392A LYS* 4.9 2.5 - - + -
393A ILE* 3.6 33.2 - - + +
396A LEU* 3.7 35.7 - - + -
398A GLN* 4.8 1.1 - - - -
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Residues in contact with TYR 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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15A ALA* 3.6 26.2 - - + -
16A HIS 4.2 0.7 - - - -
17A PRO* 3.7 41.0 - - + +
20A CYS* 3.6 20.4 - - + +
21A GLU* 4.9 1.2 + - - +
78A GLY* 4.9 0.2 - - - -
83A PRO* 3.5 7.1 - - - +
84A GLY* 2.9 38.4 + - - -
85A THR 3.3 12.1 + - - -
86A SER 3.1 4.1 + - - +
88A TRP* 1.3 91.7 - + - +
90A ASN* 1.3 66.3 + - - +
92A ALA* 3.4 5.1 + - - +
93A ALA* 3.1 22.7 + - - +
389A PRO* 2.7 35.4 + - - +
391A VAL* 3.8 17.5 - - + -
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Residues in contact with ASN 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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20A CYS* 3.3 27.4 - - - +
23A ASN* 5.2 6.7 + - - +
24A VAL* 3.6 19.3 - - + +
50A SER 3.0 28.1 + - - +
51A THR* 3.8 13.5 - - - +
55A LEU* 3.6 20.1 - - + +
86A SER* 2.7 32.7 + - - +
87A GLY 3.7 0.4 - - - +
89A TYR* 1.3 73.0 - - - +
91A SER* 1.3 56.7 + - - +
93A ALA* 3.3 4.5 + - - +
94A PHE* 2.9 26.2 + - - +
373A LEU 4.7 5.7 + - - +
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Residues in contact with SER 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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49A ALA 4.6 1.2 + - - -
50A SER* 3.4 14.0 - - - -
55A LEU* 5.6 1.5 - - - +
58A ARG* 5.1 2.9 + - - -
73A PHE* 3.2 39.0 - - - -
87A GLY 2.9 21.3 + - - -
88A TRP 3.7 4.3 - - - -
90A ASN* 1.3 73.4 - - - +
92A ALA* 1.3 65.6 + - - +
94A PHE* 3.3 7.1 + - - +
95A HIS* 3.0 32.3 + - - -
107A SER* 4.9 3.6 - - - -
393A ILE* 4.1 5.8 - - - -
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Residues in contact with ALA 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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88A TRP* 2.9 13.4 + - - +
89A TYR* 3.6 10.1 - - - +
91A SER* 1.3 77.5 - - - +
93A ALA* 1.3 62.2 + - - +
95A HIS* 3.4 3.5 + - - +
96A LYS* 3.1 21.3 + - - +
391A VAL* 3.7 30.5 - - + -
392A LYS 4.3 3.6 - - - +
393A ILE* 3.6 24.5 - - + +
394A PRO* 6.0 0.9 - - - +
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Residues in contact with ALA 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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21A GLU* 3.6 44.0 - - + -
24A VAL* 4.0 13.0 - - + -
89A TYR 3.1 11.3 + - - +
90A ASN 3.5 9.0 - - - +
92A ALA* 1.3 73.0 - - - +
94A PHE* 1.3 66.8 + - - +
96A LYS* 3.1 8.0 + - - +
97A PHE* 2.9 33.5 + - + -
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Residues in contact with PHE 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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24A VAL* 4.2 9.4 - - + +
28A ILE* 5.4 0.2 - - - -
55A LEU* 4.7 8.3 - - + -
58A ARG* 3.2 63.9 - - + +
59A ILE* 3.9 18.6 - - + -
62A ALA* 3.7 17.0 - - + -
63A PHE* 3.8 19.9 - + - -
69A THR* 3.4 19.5 - - - -
90A ASN 2.9 16.9 + - - +
91A SER* 3.3 9.4 + - - +
93A ALA* 1.3 76.9 - - - +
95A HIS* 1.3 60.9 + + + +
97A PHE* 3.3 2.8 + - - +
98A ALA* 2.9 32.0 + - + +
104A TYR 5.2 0.4 - - - -
105A ALA* 3.8 16.2 - - + -
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Residues in contact with HIS 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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58A ARG* 4.1 3.2 + - - -
91A SER 3.0 24.5 + - - +
92A ALA 3.7 7.6 - - - +
94A PHE* 1.3 84.5 - + - +
96A LYS* 1.3 63.9 + - - +
98A ALA* 3.9 0.9 - - - +
99A ALA* 3.0 26.5 + - - +
105A ALA* 3.5 32.9 + - + +
106A LYS 3.9 2.0 - - - -
107A SER* 2.7 31.6 + - - -
393A ILE* 3.4 18.9 - - + +
394A PRO* 2.8 41.7 + - + +
395A ASN* 3.4 17.0 + - - -
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Residues in contact with LYS 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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21A GLU* 2.7 41.1 + - - +
92A ALA 3.1 13.9 + - - +
93A ALA* 3.1 9.8 + - - +
95A HIS* 1.3 78.1 - - - +
97A PHE* 1.3 66.6 + - + +
99A ALA* 3.4 4.5 + - - +
100A GLN* 3.1 54.3 + - + +
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Residues in contact with PHE 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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21A GLU* 3.7 48.9 - - + -
24A VAL* 4.1 1.8 - - + -
25A LYS* 3.7 38.4 - - + -
28A ILE* 3.6 34.1 - - + -
63A PHE* 3.8 7.0 - - + -
93A ALA* 2.9 27.0 + - + +
94A PHE 4.1 1.1 - - - +
96A LYS* 1.3 83.6 - - + +
98A ALA* 1.3 66.7 + - - +
100A GLN* 3.4 27.1 + - - +
101A LYS* 3.2 22.5 + - - +
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Residues in contact with ALA 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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62A ALA* 5.8 0.2 - - + -
63A PHE* 3.7 14.0 - - + -
94A PHE* 2.9 28.3 + - + +
95A HIS 3.9 0.7 - - - +
97A PHE* 1.3 77.4 - - - +
99A ALA* 1.3 56.6 + - - +
101A LYS* 2.9 14.6 + - - +
102A GLY 3.0 0.2 + - - -
103A LEU* 2.9 45.7 + - + +
104A TYR 4.8 0.7 - - - +
105A ALA* 3.7 20.6 - - + -
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Residues in contact with ALA 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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95A HIS 3.0 18.6 + - - +
96A LYS* 3.8 4.9 - - - +
98A ALA* 1.3 76.9 - - - +
100A GLN* 1.3 63.7 + - + +
102A GLY* 3.1 12.7 + - - +
103A LEU 3.9 8.0 + - - +
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Residues in contact with GLN 100 (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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96A LYS* 3.1 47.6 + - + +
97A PHE* 3.5 27.9 - - - +
98A ALA 3.2 0.2 - - - -
99A ALA* 1.3 78.2 - - + +
101A LYS* 1.3 61.3 + - + +
102A GLY 3.3 0.6 + - - -
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Residues in contact with LYS 101 (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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28A ILE* 5.6 0.8 - - - +
32A THR* 3.9 26.5 - - - +
63A PHE* 3.9 30.1 + - + +
97A PHE 3.2 7.3 + - - +
98A ALA 2.9 9.2 + - - +
100A GLN* 1.3 78.5 - - + +
102A GLY* 1.3 62.2 + - - +
103A LEU* 3.3 14.8 + - + +
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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