Contacts of the helix formed by residues 78 - 95 (chain A) in PDB entry 1QMU
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 VAL 78 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A HIS* 3.4 31.9 - - + +
72A ASN* 4.7 1.1 - - - +
76A ASN 3.7 6.7 - - - +
77A GLU* 1.3 71.6 - - - +
79A VAL* 1.3 68.2 + - - +
80A GLY 3.0 4.0 + - - -
81A ARG* 3.1 16.1 + - - +
82A GLU* 3.3 18.5 + - + +
121A TYR* 3.4 35.4 - - + -
277A LYS 3.1 9.9 + - - +
278A TYR* 3.6 34.3 - - + -
279A PRO* 5.1 1.1 - - + -
284A LEU* 5.4 0.4 - - + -
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Residues in contact with VAL 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A GLU 3.8 0.8 - - - -
78A VAL* 1.3 76.0 - - - +
80A GLY* 1.3 65.4 + - - +
82A GLU* 3.3 5.8 + - - +
83A LEU* 3.0 37.6 + - + +
181A HIS 5.2 3.1 - - - +
182A GLY* 5.8 3.6 - - - -
273A LEU* 4.1 15.9 - - + -
274A GLY 5.8 0.9 - - - +
276A VAL 4.1 6.7 - - - +
277A LYS* 4.0 5.6 - - - +
279A PRO* 3.8 30.7 - - + -
284A LEU* 5.4 6.1 - - + -
287A TYR* 3.4 43.5 - - + -
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Residues in contact with GLY 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A GLY* 4.8 1.3 - - - -
72A ASN 5.0 4.0 - - - -
77A GLU 4.5 3.4 + - - -
78A VAL 3.0 1.6 + - - -
79A VAL* 1.3 77.6 - - - +
81A ARG* 1.3 63.5 + - - +
83A LEU* 3.0 4.2 + - - +
84A LEU* 3.0 28.6 + - - +
180A LEU* 3.9 21.3 - - - -
181A HIS 5.1 3.2 + - - -
273A LEU* 3.8 21.3 - - - +
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Residues in contact with ARG 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A HIS 2.8 28.4 + - - -
15A HIS 3.5 0.8 - - - -
16A PHE* 3.3 28.7 - - - +
19A MET* 2.9 36.4 - - + +
72A ASN* 3.0 34.4 + - + +
78A VAL 3.1 10.2 + - - +
80A GLY* 1.3 74.8 - - - +
82A GLU* 1.3 70.9 + - - +
84A LEU* 3.3 4.2 + - - +
85A LEU* 3.2 24.0 + - + +
114A PRO* 3.2 24.1 + - - +
115A SER* 3.1 19.6 + - - -
118A PRO* 4.4 3.8 - - - +
121A TYR* 3.5 42.5 - - - +
122A GLU* 4.1 1.0 + - - -
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Residues in contact with GLU 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ARG 2.9 14.4 - - - +
13A HIS* 3.2 5.0 + - - -
14A HIS* 2.7 48.1 + - - +
78A VAL* 3.7 20.6 - - + +
79A VAL 3.3 6.0 + - - +
80A GLY 3.2 0.6 - - - -
81A ARG* 1.3 81.1 - - - +
83A LEU* 1.3 61.2 + - + +
85A LEU* 3.0 12.4 + - - +
86A ASN* 2.8 40.5 + - - +
121A TYR* 3.8 8.0 + - - -
284A LEU* 4.2 26.0 - - + -
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Residues in contact with LEU 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A VAL* 3.0 26.6 + - + +
80A GLY* 3.0 5.4 + - - +
82A GLU* 1.3 76.0 - - + +
84A LEU* 1.3 58.5 + - + +
86A ASN* 3.2 8.6 + - - +
87A LEU* 2.8 28.1 + - - +
180A LEU* 5.2 4.5 - - + -
273A LEU* 3.5 31.0 - - + -
284A LEU 5.5 0.2 - - - +
287A TYR* 3.6 6.1 - - + +
288A TRP* 3.4 51.4 - - + +
291A ASN* 4.1 26.5 - - + +
295A LEU* 4.6 11.7 - - + +
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Residues in contact with LEU 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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69A TYR* 3.5 37.7 - - + +
70A ILE 3.9 5.6 - - - -
71A GLY* 3.5 20.4 - - - +
80A GLY 3.0 11.9 + - - +
81A ARG 3.7 7.2 - - - +
83A LEU* 1.3 72.8 - - - +
85A LEU* 1.3 62.1 + - - +
87A LEU* 3.2 12.5 + - + +
88A ILE* 2.9 33.2 + - - +
112A ILE* 3.6 21.1 - - + +
113A MET 3.5 25.8 - - - +
114A PRO* 3.9 10.5 - - + -
180A LEU* 4.0 14.6 - - + -
295A LEU* 5.3 3.6 - - + -
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Residues in contact with LEU 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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14A HIS* 3.6 32.1 - - + +
19A MET* 3.9 28.0 - - + -
22A PHE* 3.5 39.5 - - + -
23A LEU* 4.3 6.1 - - + -
81A ARG 3.2 13.6 + - - +
82A GLU* 3.0 31.9 + - - +
84A LEU* 1.3 74.3 - - - +
86A ASN* 1.3 69.4 + - - +
88A ILE* 3.0 6.4 + - + +
89A GLU 2.9 19.9 + - - -
114A PRO* 4.0 17.9 - - + -
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Residues in contact with ASN 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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8A PRO* 3.5 13.3 - - + +
10A ASP 3.8 21.0 + - - -
11A PHE* 3.2 32.5 - - - +
22A PHE* 5.8 0.8 - - - -
82A GLU* 2.8 27.9 + - - +
83A LEU* 3.3 14.2 - - - +
85A LEU* 1.3 78.3 - - - +
87A LEU* 1.3 51.7 + - - +
89A GLU* 3.3 6.7 + - - +
90A TYR* 2.8 35.3 + - - +
284A LEU* 5.0 1.6 - - - +
288A TRP* 3.3 29.4 - - + +
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Residues in contact with LEU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A TYR* 3.9 29.4 - - + -
83A LEU 2.8 13.2 + - - +
84A LEU* 3.3 16.6 - - + +
86A ASN* 1.3 72.5 - - - +
88A ILE* 1.3 68.9 + - - +
89A GLU 3.1 0.9 - - - -
90A TYR* 3.2 2.2 + - + -
91A LEU* 2.8 57.5 + - + +
112A ILE* 3.8 19.7 - - + -
288A TRP* 3.8 17.9 - - + -
295A LEU* 4.7 14.1 - - + -
296A LEU* 4.5 17.7 - - + -
299A ILE* 4.7 5.6 - - + -
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Residues in contact with ILE 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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22A PHE* 4.3 7.2 - - + -
23A LEU* 4.6 12.1 - - + -
26A TYR* 4.2 25.4 - - + -
51A MET* 3.3 42.0 - - + -
53A ILE* 4.1 11.4 - - + -
84A LEU 2.9 25.8 + - - +
85A LEU* 3.4 10.1 - - + +
87A LEU* 1.3 73.4 - - - +
89A GLU* 1.3 69.2 + - - +
91A LEU* 3.7 1.2 - - - +
92A CYS* 3.0 26.6 + - - -
112A ILE* 3.6 30.1 - - + +
114A PRO* 5.2 2.0 - - + -
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Residues in contact with GLU 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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7A GLN 4.3 0.3 - - - +
8A PRO* 3.1 18.5 - - + +
9A VAL* 3.1 22.9 + - - +
10A ASP* 3.6 26.3 + - - +
22A PHE* 3.8 7.6 - - + -
26A TYR* 3.0 39.0 + - + +
85A LEU 2.9 10.9 + - - +
86A ASN* 3.3 11.2 + - - +
88A ILE* 1.3 78.0 - - - +
90A TYR* 1.3 67.5 + - - +
91A LEU 2.8 1.2 + - - -
92A CYS* 2.9 0.7 + - - +
93A LYS* 2.8 54.5 + - + +
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Residues in contact with TYR 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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5A ALA* 3.6 18.5 - - + +
6A VAL 3.4 24.5 - - - -
7A GLN* 3.5 26.6 + - - -
8A PRO* 4.0 6.4 - - + +
86A ASN 2.8 20.4 + - - +
87A LEU* 3.7 7.2 - - + +
89A GLU* 1.3 73.8 - - - +
91A LEU* 1.3 69.2 + - + +
93A LYS* 4.7 2.0 - - - +
94A ASN* 2.8 39.4 + - - +
98A ASP* 4.5 2.4 + - - -
100A GLU* 4.6 6.9 + - - -
101A VAL* 3.5 27.7 - - + +
288A TRP* 3.6 30.7 - + + -
292A ARG* 3.9 9.1 - - - -
293A ARG* 4.9 0.3 + - - -
296A LEU* 4.2 24.1 - - + +
997A SO4 4.9 4.7 + - - -
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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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53A ILE* 3.7 37.0 - - + -
87A LEU* 2.8 50.6 + - + +
88A ILE 3.7 2.7 - - - +
89A GLU 2.8 2.0 + - - -
90A TYR* 1.3 72.7 - - + +
92A CYS* 1.3 64.3 + - - +
95A PHE* 3.0 23.8 + - - +
101A VAL* 3.3 32.1 - - + +
104A LEU* 4.8 11.7 - - + -
105A VAL* 4.7 8.3 - - + -
110A ILE* 4.5 15.9 - - + -
112A ILE* 4.3 6.1 - - + -
296A LEU* 4.8 9.0 - - + -
299A ILE* 5.4 2.0 - - + -
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Residues in contact with CYS 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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26A TYR* 3.9 16.2 - - + -
30A TYR* 3.3 44.9 - - + -
33A ILE* 5.4 5.4 - - - -
34A THR* 3.6 31.9 - - - -
53A ILE* 4.5 8.5 - - - -
88A ILE* 3.0 28.2 + - - +
89A GLU 2.9 6.2 + - - +
91A LEU* 1.3 75.0 - - - +
93A LYS* 1.3 62.9 + - - +
95A PHE* 3.7 14.4 + - - +
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Residues in contact with LYS 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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6A VAL* 4.6 26.0 - - + +
7A GLN 5.3 1.1 + - - +
8A PRO* 5.8 0.2 - - + -
9A VAL* 4.2 13.1 - - - +
25A ARG* 5.1 9.3 - - - +
26A TYR* 3.2 28.4 + - + -
29A GLU* 6.0 0.7 - - - -
30A TYR* 3.6 21.0 - - - +
89A GLU* 2.8 48.8 + - + +
90A TYR* 4.2 3.6 - - - +
92A CYS* 1.3 75.2 - - - +
94A ASN* 1.3 66.3 + - - +
95A PHE 3.7 1.9 + - - +
97A THR* 4.2 9.5 + - - -
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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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5A ALA* 3.1 17.2 - - - +
6A VAL* 2.6 54.8 + - - +
90A TYR* 2.8 37.7 + - - +
93A LYS* 1.3 78.9 - - - +
95A PHE* 1.3 62.5 + - - +
96A GLY 3.1 0.3 + - - -
97A THR* 3.2 6.7 + - - +
98A ASP* 2.7 48.1 + - + +
101A VAL* 3.7 12.1 - - + -
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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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33A ILE* 3.2 42.8 - - + -
55A ASP* 4.0 15.0 - - + -
91A LEU 3.0 17.1 + - - +
92A CYS* 4.0 11.1 - - - +
93A LYS 3.4 4.1 - - - +
94A ASN* 1.3 75.7 - - - +
96A GLY* 1.3 59.3 + - - +
97A THR* 3.3 5.6 + - - -
101A VAL* 3.6 6.0 - - + +
102A THR* 3.5 35.7 - - + -
105A VAL* 3.5 33.7 - - + -
106A GLN* 3.9 13.2 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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