Contacts of the helix formed by residues 75 - 90 (chain A) in PDB entry 2QU7
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
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73A ASP* 3.0 23.5 + - - +
74A GLN* 1.3 76.4 - - - +
76A PRO* 1.4 70.1 - - - +
77A PHE* 2.8 32.2 + - - +
78A PHE* 2.9 31.9 + - + +
79A THR* 3.9 3.6 + - - +
251A ASN* 4.1 13.3 + - - +
252A HIS* 3.6 14.2 - - - +
253A LEU* 4.2 13.2 - - + +
279A ASP* 2.9 27.5 + - - +
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Residues in contact with PRO 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A GLN 3.3 9.1 - - - +
75A ASN* 1.4 88.7 - - - +
77A PHE* 1.3 61.4 + - - +
78A PHE 3.1 0.4 - - - -
79A THR* 3.2 14.7 + - + +
80A GLU* 2.9 34.7 + - + +
252A HIS* 3.6 37.9 - - + +
253A LEU* 4.9 2.2 - - + -
279A ASP* 6.1 0.2 - - + -
280A ASP 5.0 9.4 - - - +
281A SER* 5.2 4.3 - - - +
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Residues in contact with PHE 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ASN* 2.8 23.8 + - - +
76A PRO* 1.3 79.2 - - - +
78A PHE* 1.3 91.0 + + - +
80A GLU* 3.6 9.1 + - - +
81A VAL* 3.1 39.1 + - + +
146A LEU* 4.7 1.6 - - + -
147A ASP* 3.7 20.2 - - + -
279A ASP* 4.4 16.4 - - + +
280A ASP 5.5 2.1 + - - -
296A GLN* 3.6 45.3 - - + -
298A VAL* 3.8 20.6 - - + -
301A MET* 3.8 27.4 - - + -
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Residues in contact with PHE 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A PHE* 3.5 13.2 - + - -
71A VAL* 4.0 21.3 - - + -
72A PRO* 3.7 22.7 - - + -
73A ASP* 3.3 37.0 - - - +
75A ASN* 2.9 23.4 + - + +
77A PHE* 1.3 103.5 - + - +
79A THR* 1.3 61.5 + - + +
81A VAL* 3.3 3.3 + - + +
82A LEU* 2.8 28.8 + - - +
126A VAL* 3.7 31.9 - - + -
146A LEU* 4.7 2.0 - - + -
147A ASP* 3.9 17.0 - - + -
148A ARG* 4.3 5.6 - - - -
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Residues in contact with THR 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A GLN* 6.0 4.9 - - + +
75A ASN 3.9 5.1 + - - +
76A PRO* 3.2 18.0 + - + +
78A PHE* 1.3 76.1 - - + +
80A GLU* 1.3 65.9 + - - +
82A LEU* 3.2 19.9 + - + +
83A THR* 3.0 28.8 + - - -
98A VAL* 6.2 2.7 - - + -
74B GLN* 4.2 20.8 + - + +
79B THR* 5.0 16.6 - - + -
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Residues in contact with GLU 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A PRO* 2.9 27.5 + - + +
77A PHE* 3.7 7.4 - - - +
79A THR* 1.3 79.7 + - - +
81A VAL* 1.3 59.9 + - - +
83A THR* 3.6 5.9 + - - -
84A GLU* 3.5 22.0 + - - +
280A ASP* 4.1 29.5 - - - +
281A SER* 4.9 4.9 - - - -
282A TYR* 5.4 9.7 - - - -
298A VAL* 4.1 30.9 - - + +
74B GLN* 4.3 13.2 - - - +
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Residues in contact with VAL 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A PHE* 4.7 3.6 - - + -
77A PHE* 3.1 41.9 + - + +
78A PHE* 3.3 5.8 + - - +
80A GLU* 1.3 72.1 - - - +
82A LEU* 1.3 67.0 + - - +
84A GLU* 3.1 4.7 + - - +
85A ILE* 2.9 40.3 + - + +
146A LEU* 3.8 20.2 - - + -
298A VAL* 4.0 27.1 - - + +
301A MET* 4.4 6.5 - - + -
302A GLY* 4.0 15.0 - - - +
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Residues in contact with LEU 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A PHE* 3.9 14.8 - - + -
78A PHE 2.8 18.1 + - - +
79A THR* 3.3 20.4 - - + +
81A VAL* 1.3 76.4 - - - +
83A THR* 1.3 54.9 + - - +
85A ILE* 3.0 6.4 + - - -
86A SER* 2.8 45.3 + - - +
96A VAL* 3.4 37.2 - - + +
98A VAL* 3.1 34.3 - - + -
74B GLN* 6.5 1.1 - - + -
100B SER* 5.9 8.7 - - - +
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Residues in contact with THR 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A THR 3.0 13.0 + - - -
80A GLU* 3.8 8.7 - - - -
81A VAL 3.3 0.2 - - - -
82A LEU* 1.3 78.3 - - - +
84A GLU* 1.3 63.5 + - - +
86A SER* 3.5 7.2 + - - -
87A HIS* 3.0 30.3 + - + +
74B GLN* 3.0 36.5 + - - +
102B GLU* 4.6 18.8 + - + +
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Residues in contact with GLU 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A GLU 3.5 12.3 + - - +
81A VAL 3.1 9.6 + - - +
83A THR* 1.3 79.7 - - - +
85A ILE* 1.3 63.3 + - - +
87A HIS* 3.5 12.6 + - - +
88A GLU* 3.4 21.7 + - - +
298A VAL* 4.0 5.2 - - + +
299A LYS* 3.7 49.9 - - + +
302A GLY* 3.9 19.6 - - - +
303A GLN* 4.5 9.5 + - - +
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Residues in contact with ILE 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A PHE* 4.4 15.0 - - + -
81A VAL* 2.9 37.3 + - + +
82A LEU* 3.6 7.9 - - - +
84A GLU* 1.3 75.3 - - - +
86A SER* 1.3 58.1 + - - +
88A GLU 3.4 1.7 + - - -
89A CYS* 2.9 40.3 + - - +
96A VAL* 3.8 20.4 - - + -
124A ILE* 4.0 27.4 - - + -
146A LEU* 3.9 15.7 - - + -
302A GLY* 3.5 24.9 - - - +
305A ALA* 4.5 3.8 - - + -
306A ALA* 3.8 7.2 - - + +
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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
----------------------------------------------------------
82A LEU* 2.8 29.1 + - - +
83A THR* 3.6 8.5 - - - -
85A ILE* 1.3 71.3 - - - +
87A HIS* 1.3 65.4 + - - +
89A CYS* 4.1 0.2 - - - +
90A GLN* 3.1 32.9 + - - +
94A LEU 4.9 0.6 - - - +
96A VAL* 3.5 31.1 + - - +
100B SER 6.1 0.4 - - - -
107B LYS* 4.9 12.4 + - - +
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Residues in contact with HIS 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A THR* 3.0 18.5 + - + +
84A GLU* 3.8 15.5 - - - +
85A ILE 3.3 0.4 - - - -
86A SER* 1.3 76.8 - - - +
88A GLU* 1.3 65.1 + - + +
90A GLN* 3.3 31.3 + - - +
91A LYS* 3.9 25.3 + - - +
303A GLN* 5.3 5.2 - - - -
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Residues in contact with GLU 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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84A GLU 3.4 10.2 + - - +
86A SER 3.3 0.6 - - - -
87A HIS* 1.3 78.0 - - - +
89A CYS* 1.3 62.6 + - - +
91A LYS* 3.0 56.8 + - - +
92A HIS* 4.1 14.4 + - + +
303A GLN* 2.8 43.2 + - - +
306A ALA* 3.5 28.7 - - + -
307A LYS* 3.9 19.1 - - + +
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Residues in contact with CYS 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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67A ILE* 3.4 31.4 - - + -
85A ILE* 2.9 34.3 + - - +
86A SER 4.1 2.0 - - - +
88A GLU* 1.3 73.5 - - - +
90A GLN* 1.3 57.6 + - - +
91A LYS 3.1 0.4 - - - -
92A HIS* 2.9 29.7 + - - +
94A LEU* 3.3 27.4 + - + +
96A VAL* 4.3 6.3 - - + -
306A ALA* 3.8 22.7 - - - -
309A ILE* 4.2 5.8 - - - -
310A TYR* 6.1 1.1 - - - -
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Residues in contact with GLN 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 SER* 3.1 22.8 + - - +
87A HIS* 3.3 32.4 + - - +
89A CYS* 1.3 72.9 - - - +
91A LYS* 1.3 62.1 + - + +
92A HIS 3.0 5.4 - - - -
93A HIS* 3.0 20.3 + - - +
94A LEU 3.3 12.5 + - - +
95A HIS* 4.8 6.5 - - + +
107B LYS* 3.1 38.2 + - + +
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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
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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