Contacts of the helix formed by residues 75 - 93 (chain A) in PDB entry 2QY7
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 ASN 75 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASP* 3.2 31.2 + - - +
71A ASP 4.6 1.7 - - - +
72A ASN 3.7 4.8 + - - +
73A LYS 3.6 0.8 - - - -
74A LYS* 1.3 92.2 + - - +
76A TRP* 1.3 63.7 + - - +
77A ARG 3.4 2.2 - - - -
78A ARG* 3.4 59.0 + - + +
79A VAL* 3.5 12.1 + - - +
114A TYR* 3.9 3.1 - - - -
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Residues in contact with TRP 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LYS 3.9 2.0 - - - -
75A ASN* 1.3 73.9 - - - +
77A ARG* 1.3 113.7 + - + +
79A VAL* 3.1 6.1 + - - +
80A TYR* 2.9 42.3 + + + -
114A TYR* 3.4 27.2 + - + +
116A PHE* 3.5 44.1 - + + -
118A ASP* 5.4 1.8 - - - +
124A GLN* 3.5 51.5 - - + +
127A ASN* 4.0 20.6 - - + -
128A ILE* 3.6 13.7 - - + +
20B ASN 5.4 0.9 + - - -
59B GLU* 4.4 3.8 - - - -
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Residues in contact with ARG 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ASN 4.7 2.0 - - - +
34A ASP* 4.2 20.0 - - - +
35A ASP 4.3 2.2 - - - -
36A PRO* 3.8 37.0 + - - +
75A ASN 3.4 0.4 - - - -
76A TRP* 1.3 128.9 - - + +
78A ARG* 1.3 53.1 + - - +
80A TYR* 3.2 7.4 + - + +
81A LYS* 2.7 51.2 + - + +
124A GLN* 4.1 1.0 - - - +
20B ASN* 3.2 24.5 + - - +
22B SER* 3.4 10.3 - - - +
25B GLU* 2.8 26.9 + - - -
59B GLU* 2.9 23.8 + - - -
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Residues in contact with ARG 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A THR* 3.4 25.3 - - - +
33A ASN 4.4 2.4 + - - -
34A ASP* 4.5 8.5 + - - +
67A ARG* 3.4 71.3 + - + +
70A LYS 4.2 4.8 + - - -
71A ASP* 3.0 30.5 + - - +
72A ASN* 4.5 2.6 - - - +
75A ASN* 3.4 49.6 + - + +
77A ARG* 1.3 78.0 - - - +
79A VAL* 1.3 55.4 + - - +
81A LYS 3.9 0.3 - - - -
82A SER* 3.0 30.5 + - - -
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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
----------------------------------------------------------
67A ARG 4.3 5.4 - - - +
68A MET* 3.5 25.8 - - + +
72A ASN* 3.6 25.4 - - + +
75A ASN 3.6 13.7 - - - +
76A TRP* 3.1 7.9 + - - +
78A ARG* 1.3 72.7 - - + +
80A TYR* 1.3 67.3 + - - +
82A SER* 2.5 24.3 + - - -
83A LEU* 3.0 9.6 + - + +
111A LEU* 4.1 18.6 - - + -
114A TYR* 4.1 7.0 - - + +
128A ILE* 4.0 29.6 - - + -
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Residues in contact with TYR 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A TRP* 2.9 28.2 + + + +
77A ARG* 3.6 9.9 - - - +
79A VAL* 1.3 76.4 - - - +
81A LYS* 1.3 60.7 + - + +
83A LEU* 3.1 7.9 + - + +
84A LEU* 2.8 52.1 + - + +
127A ASN* 3.4 32.3 - - + -
128A ILE* 3.1 26.3 - - + +
131A LYS* 3.6 22.4 - - + +
55B GLU 3.8 10.7 + - - -
58B PRO* 3.7 28.2 - - - +
59B GLU* 3.6 30.0 + - + -
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Residues in contact with LYS 81 (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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30A GLU 5.0 0.8 + - - -
31A ALA 3.5 25.4 - - - +
32A THR* 4.0 5.3 - - - +
33A ASN* 2.9 41.7 + - - +
35A ASP* 2.8 26.9 + - - +
37A TRP 3.1 20.7 + - - -
38A GLY* 3.8 19.5 - - - +
39A PRO* 3.9 5.8 - - + +
77A ARG* 2.7 29.9 + - + +
78A ARG 4.0 2.7 - - - +
80A TYR* 1.3 73.5 - - + +
82A SER* 1.3 60.5 + - - +
84A LEU* 3.7 12.0 - - + +
85A LEU* 2.9 30.1 + - - +
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Residues in contact with SER 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A THR* 3.6 18.1 - - - +
64A LEU* 4.2 12.1 - - - +
67A ARG 4.6 0.4 - - - -
68A MET* 3.0 45.2 - - - +
78A ARG 3.0 15.9 + - - -
79A VAL 2.5 19.1 + - - -
81A LYS* 1.3 75.5 - - - +
83A LEU* 1.3 56.3 + - - +
85A LEU* 3.5 3.8 + - - +
86A LEU* 2.8 30.3 + - - +
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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
----------------------------------------------------------
68A MET* 3.7 26.2 - - + -
79A VAL* 3.0 20.3 + - + +
80A TYR* 3.1 10.1 + - - +
82A SER* 1.3 76.1 + - - +
84A LEU* 1.3 58.1 + - - +
86A LEU 3.3 0.5 + - - -
87A ALA* 2.9 30.0 + - - +
108A LEU* 3.8 20.2 - - + -
111A LEU* 4.4 1.8 - - + -
128A ILE* 3.9 43.7 - - + +
131A LYS* 4.0 17.0 - - + -
132A VAL* 3.9 18.2 - - + +
135A LEU* 3.5 18.5 - - + +
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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
----------------------------------------------------------
38A GLY 4.2 17.9 - - - +
39A PRO* 4.3 8.1 - - + -
44A MET* 4.2 4.0 - - - +
80A TYR* 2.8 51.5 + - + +
81A LYS* 3.3 10.9 + - + +
83A LEU* 1.3 74.5 - - - +
85A LEU* 1.3 62.1 + - - +
87A ALA* 3.3 7.7 + - + +
88A TYR* 3.0 22.5 + - - +
131A LYS* 3.9 21.8 - - + +
55B GLU* 3.8 52.7 - - + +
59B GLU* 5.7 0.4 - - - +
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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
----------------------------------------------------------
28A VAL* 4.2 17.3 - - + -
31A ALA* 4.1 11.7 - - + -
32A THR* 4.6 6.5 - - + -
39A PRO* 4.6 5.8 - - + +
44A MET* 3.8 33.6 - - + -
47A ILE* 3.9 33.7 - - + -
64A LEU* 4.0 17.5 - - + -
81A LYS 2.9 18.1 + - - +
82A SER* 3.7 3.8 - - - +
84A LEU* 1.3 76.1 - - - +
86A LEU* 1.3 63.6 + - - +
88A TYR* 3.0 3.9 + - + +
89A LEU* 2.9 47.4 + - + +
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Residues in contact with LEU 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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61A MET* 4.4 16.8 - - + -
64A LEU* 4.2 15.0 - - + +
65A TRP* 3.8 24.2 - - + -
68A MET* 4.0 7.6 - - + -
82A SER 2.8 22.4 + - - +
83A LEU 3.3 4.9 + - - +
85A LEU* 1.3 71.9 - - - +
87A ALA* 1.3 58.1 + - - +
89A LEU* 3.2 2.0 + - + -
90A ILE* 2.8 53.0 + - + +
97A VAL* 4.0 15.3 - - + -
101A ALA* 4.6 7.0 - - + -
108A LEU* 4.0 19.1 - - + -
135A LEU* 3.9 16.8 - - + -
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Residues in contact with ALA 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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83A LEU 2.9 14.9 + - - +
84A LEU* 3.5 9.2 - - + +
86A LEU* 1.3 75.0 - - - +
88A TYR* 1.3 62.9 + - - +
90A ILE* 3.5 3.0 + - - +
91A ARG* 3.4 28.8 + - - +
131A LYS* 4.0 23.6 - - - +
135A LEU* 3.8 23.9 - - + +
138A PHE* 5.0 1.6 - - + -
54B TYR* 4.1 13.0 - - + +
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Residues in contact with TYR 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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41A GLY* 4.1 8.8 + - - -
44A MET* 3.4 67.1 - - + -
45A GLY* 3.5 20.1 - - - -
48A ALA* 3.8 6.7 - - + +
84A LEU 3.0 8.4 + - - +
85A LEU 3.0 7.2 + - - +
87A ALA* 1.3 75.6 - - - +
89A LEU* 1.3 63.9 + - + +
91A ARG* 3.2 4.9 + - - +
92A ASN* 2.8 72.6 + - + +
54B TYR* 4.8 2.6 + - - -
55B GLU* 5.1 4.7 - - - +
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Residues in contact with LEU 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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44A MET 4.2 5.2 - - - +
47A ILE* 4.0 17.9 - - + -
48A ALA* 3.5 40.4 - - + +
51A THR* 4.1 8.7 - - + -
60A LEU* 4.1 11.4 - - + -
61A MET* 4.6 5.8 - - - -
64A LEU* 3.8 28.3 - - + -
85A LEU* 2.9 28.3 + - + +
86A LEU* 3.7 4.0 - - - +
88A TYR* 1.3 75.9 - - + +
90A ILE* 1.3 60.9 + - - +
93A GLY* 2.8 30.8 + - - +
97A VAL* 3.8 19.3 - - + +
149A ARG* 4.0 0.2 + - - -
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Residues in contact with ILE 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 LEU* 2.8 36.4 + - + +
87A ALA* 3.9 5.4 - - - +
88A TYR 3.3 0.4 - - - -
89A LEU* 1.3 75.8 - - - +
91A ARG* 1.3 56.7 + - - +
97A VAL* 3.8 19.5 - - + +
98A VAL* 3.9 9.2 - - + +
101A ALA* 3.9 19.7 - - + -
108A LEU* 6.0 0.2 - - + -
135A LEU* 3.6 26.5 - - + -
138A PHE* 4.0 16.4 - - + -
139A ALA* 4.7 10.5 - - + -
145A LEU* 3.6 26.7 - - + -
149A ARG* 2.8 29.6 + - - +
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Residues in contact with ARG 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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87A ALA* 3.4 15.3 + - - +
88A TYR* 3.2 7.5 + - - +
89A LEU 3.2 0.4 - - - -
90A ILE* 1.3 78.5 - - - +
92A ASN* 1.3 71.7 + - - +
93A GLY 3.8 0.4 - - - -
138A PHE* 3.8 30.8 - - + -
144A ARG* 4.5 11.5 - - - +
148A GLU* 2.5 40.7 + - + +
149A ARG* 3.8 24.7 + - - +
152A ALA* 3.6 21.3 - - + +
54B TYR* 3.3 42.8 + - - -
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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
----------------------------------------------------------
48A ALA* 4.0 7.3 - - + +
52A PHE* 3.8 13.7 - - - -
88A TYR* 2.8 73.4 + - + +
91A ARG* 1.3 86.2 - - - +
93A GLY* 1.3 64.0 + - - +
152A ALA* 3.6 21.4 - - - +
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Residues in contact with GLY 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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48A ALA* 4.0 8.3 - - - -
51A THR* 3.4 13.2 - - - -
52A PHE* 3.5 11.8 - - - -
89A LEU* 2.8 23.6 + - - +
92A ASN* 1.3 76.6 - - - +
94A SER* 1.3 57.5 + - - -
97A VAL* 4.7 0.7 - - - -
149A ARG* 2.8 33.1 + - - -
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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
------------------------------------------------------------
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