Contacts of the helix formed by residues 87 - 101 (chain A) in PDB entry 3QU3
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 GLU 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A ARG 6.0 0.4 - - - -
68A TRP* 3.9 26.4 - - + -
83A ALA 3.5 16.4 - - - +
84A GLU 2.8 8.1 + - - +
86A ARG* 1.3 88.8 - - - +
88A ARG* 1.3 59.1 + - - +
89A ARG 3.3 2.2 - - - -
90A GLY* 3.3 6.2 + - - -
91A TRP* 3.1 51.8 + - + -
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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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50A LEU* 2.7 54.7 + - + +
51A ASP* 3.5 3.6 - - - +
52A GLU* 3.3 33.2 - - - +
55A ALA* 3.5 24.8 - - + +
58A PHE* 4.3 0.9 - - - -
81A GLU* 2.8 34.4 + - - +
84A GLU* 3.3 35.0 + - - +
85A ARG* 3.3 31.4 + - - +
87A GLU* 1.3 75.6 - - - +
89A ARG* 1.3 60.7 + - - +
91A TRP* 3.7 18.1 - - + +
92A LYS* 3.0 28.1 + - - +
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Residues in contact with ARG 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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45A PHE* 3.9 6.5 - - - +
46A GLY 2.6 31.9 + - - +
47A ARG 2.9 13.0 + - - -
48A ARG 2.5 31.2 + - - -
49A ASP* 4.4 13.3 + - - +
50A LEU* 3.3 20.5 - - + +
85A ARG 4.7 2.9 + - - +
86A ARG 5.2 1.7 + - - +
87A GLU 3.3 1.2 - - - -
88A ARG* 1.3 74.8 - - + +
90A GLY* 1.3 59.5 + - - +
92A LYS* 3.4 25.8 + - - +
93A THR* 3.0 32.3 + - - +
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Residues in contact with GLY 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 ARG 5.7 0.4 + - - -
87A GLU 3.3 7.3 + - - -
89A ARG* 1.3 76.7 - - - +
91A TRP* 1.3 59.8 + - - +
93A THR* 3.3 7.5 + - - +
94A ASN* 2.9 30.7 + - - +
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Residues in contact with TRP 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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55A ALA* 4.7 3.6 - - + -
58A PHE* 3.7 19.1 - - + +
59A LYS* 3.4 42.8 - - + -
61A TRP* 5.3 0.2 - - - -
62A ALA* 3.4 27.9 - - + +
65A ARG* 4.3 8.7 + - - +
67A ARG* 4.7 8.4 + - + +
68A TRP* 3.6 42.4 - + + -
84A GLU* 4.3 12.1 - - + -
87A GLU* 3.1 40.4 + - + +
88A ARG* 3.7 33.4 - - + +
89A ARG 3.3 0.2 - - - -
90A GLY* 1.3 74.4 - - - +
92A LYS* 1.3 58.8 + - - +
94A ASN* 3.7 4.4 - - - +
95A PHE* 3.0 31.4 + - - +
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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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45A PHE* 3.8 23.6 - - + -
50A LEU* 4.0 3.1 - - + -
58A PHE* 3.3 30.2 - - + -
88A ARG 3.0 14.4 + - - +
89A ARG* 3.5 31.1 + - - +
90A GLY 3.3 0.2 - - - -
91A TRP* 1.3 76.1 - - - +
93A THR* 1.3 91.1 + - - +
95A PHE* 3.6 1.0 + - - +
96A ARG* 3.1 64.1 + - - +
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Residues in contact with THR 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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89A ARG 3.0 14.3 + - - -
90A GLY* 3.6 8.1 - - - +
92A LYS* 1.3 101.7 + - - +
94A ASN* 1.3 63.4 + - - +
96A ARG* 4.1 2.9 - - - +
97A CYS* 3.1 44.1 + - - -
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Residues in contact with ASN 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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61A TRP* 3.2 21.0 + - - -
65A ARG* 3.4 35.1 + - - +
67A ARG* 5.8 0.4 - - - +
90A GLY 2.9 17.5 + - - +
91A TRP 3.7 3.6 - - - +
92A LYS 3.3 0.2 - - - -
93A THR* 1.3 79.3 - - - +
95A PHE* 1.3 61.6 + - - +
97A CYS* 3.9 4.9 - - - +
98A ALA* 3.1 21.7 + - - +
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Residues in contact with PHE 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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12A PHE* 3.4 35.5 - + - -
15A TRP* 4.1 2.0 - + - -
16A LEU* 3.9 15.3 - - + -
28A LEU* 5.7 0.2 - - + -
40A VAL* 4.2 16.2 - - + -
41A PRO 5.6 0.9 - - - -
42A TRP* 5.3 1.6 - + - -
57A ILE* 3.8 28.5 - - + -
58A PHE* 3.6 34.3 - + + -
61A TRP* 3.9 26.1 - - + -
91A TRP 3.0 17.8 + - - +
92A LYS 3.8 2.7 - - - +
94A ASN* 1.3 73.8 + - - +
96A ARG* 1.3 69.1 + - + +
98A ALA* 3.1 4.9 + - - +
99A LEU* 2.9 47.7 + - + +
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Residues in contact with ARG 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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41A PRO 4.8 1.2 + - - -
42A TRP* 3.7 55.2 - - + +
43A LYS 2.8 45.1 + - - +
44A HIS* 4.9 4.4 + - - +
45A PHE* 3.9 5.9 - - - -
58A PHE* 3.9 19.0 - - - -
92A LYS* 3.1 45.8 + - + +
93A THR* 4.2 3.6 - - - +
95A PHE* 1.3 87.5 - - + +
97A CYS* 1.3 58.6 + - - +
99A LEU* 3.2 6.4 + - - +
100A HIS* 2.9 27.7 + - - +
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Residues in contact with CYS 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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93A THR* 3.1 39.7 + - - +
94A ASN* 3.9 5.4 - - - +
96A ARG* 1.3 73.8 - - - +
98A ALA* 1.3 65.6 + - - +
100A HIS* 3.3 7.9 + - - +
101A SER* 3.0 29.9 + - - +
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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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12A PHE* 3.8 28.7 - - + +
61A TRP* 4.0 11.0 - - + +
94A ASN* 3.1 15.5 + - - +
95A PHE 3.1 10.2 + - - +
97A CYS* 1.3 76.1 - - - +
99A LEU* 1.3 61.6 + - - +
101A SER* 3.3 6.6 + - - -
102A THR* 2.8 27.2 + - - -
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Residues in contact with LEU 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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12A PHE* 3.5 18.6 - - + -
16A LEU* 4.2 9.6 - - + -
40A VAL* 4.2 13.7 - - + -
42A TRP* 3.9 22.2 - - + -
95A PHE* 2.9 35.3 + - + +
96A ARG* 3.5 9.9 - - - +
98A ALA* 1.3 79.3 - - - +
100A HIS* 1.3 53.7 + - - +
102A THR* 3.1 11.9 + - - -
105A PHE* 3.8 17.3 - - + -
122A TYR* 3.6 34.3 - - + +
135A NA 2.8 24.5 - - - -
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Residues in contact with HIS 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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42A TRP* 6.1 0.2 - - - -
96A ARG 2.9 16.0 + - - +
97A CYS* 3.7 7.9 - - - +
98A ALA 3.3 0.2 - - - -
99A LEU* 1.3 76.5 - - - +
101A SER* 1.3 68.6 + - - +
102A THR 3.1 5.6 + - - -
103A GLY* 4.5 2.4 + - - -
135A NA 3.5 12.4 - - - -
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Residues in contact with SER 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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97A CYS* 3.0 17.8 + - - +
98A ALA* 3.3 7.6 + - - -
99A LEU 3.2 0.4 - - - -
100A HIS* 1.3 85.8 - - - +
102A THR* 1.3 57.6 + - - +
103A GLY* 3.5 5.9 + - - -
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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