Contacts of the helix formed by residues 83 - 95 (chain A) in PDB entry 1QD9
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 GLN 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A ILE* 3.6 46.3 - - + +
78A ILE* 5.0 0.9 - - + -
80A ASP* 2.9 36.9 + - + +
82A GLU* 1.3 80.0 - - + +
84A PHE* 1.3 61.6 + - - +
85A ALA 3.4 2.7 - - - -
86A GLU* 3.3 20.2 + - - +
87A VAL* 3.1 25.0 + - + +
115A LEU* 4.3 21.7 - - - +
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Residues in contact with PHE 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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78A ILE* 4.4 7.6 - - + -
80A ASP 4.0 0.4 + - - -
81A MET* 3.0 45.1 + - + +
82A GLU 3.3 1.4 - - - -
83A GLN* 1.3 77.1 - - - +
85A ALA* 1.3 61.4 + - - +
87A VAL* 3.2 5.0 + - - +
88A ASN* 2.8 53.6 + - + -
102A ARG* 3.5 25.1 - - - -
104A CYS* 4.2 24.2 - - + -
111B PRO* 4.8 15.0 - - + -
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Residues in contact with ALA 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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82A GLU 4.9 1.2 + - - +
83A GLN 3.4 0.8 - - - -
84A PHE* 1.3 84.1 - - - +
86A GLU* 1.3 65.8 + - + +
88A ASN* 3.6 4.1 - - - +
89A GLU* 2.9 30.5 + - - +
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Residues in contact with GLU 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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46A ILE* 3.7 26.0 - - + +
47A LYS* 4.0 28.5 - - - +
82A GLU 3.7 6.6 - - - +
83A GLN* 3.5 33.5 + - - +
84A PHE 3.2 0.4 - - - -
85A ALA* 1.3 82.4 + - + +
87A VAL* 1.3 66.6 + - - +
89A GLU* 3.4 10.8 + - - +
90A VAL* 3.4 17.3 + - - +
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Residues in contact with VAL 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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46A ILE* 3.5 31.0 - - + -
50A THR* 3.8 24.0 - - + +
76A VAL* 4.5 10.3 - - + -
78A ILE* 4.2 21.5 - - + -
83A GLN* 3.1 15.1 + - + +
84A PHE* 3.7 7.4 - - - +
86A GLU* 1.3 76.2 - - - +
88A ASN* 1.3 59.1 + - - +
90A VAL* 3.2 4.7 + - - +
91A TYR* 2.9 31.6 + - + +
116A VAL* 4.4 13.9 - - + -
118A ILE* 5.3 2.7 - - + -
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Residues in contact with ASN 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 PHE* 2.8 36.8 + - + +
85A ALA* 3.6 6.5 - - - +
87A VAL* 1.3 79.0 - - - +
89A GLU* 1.3 57.7 + - - +
91A TYR* 3.5 4.4 - - - +
92A GLY* 2.8 28.1 + - - -
102A ARG* 2.9 30.8 + - - +
14B ILE 5.5 0.6 + - - -
15B GLY* 4.6 4.9 - - - -
16B PRO* 3.1 25.7 - - - +
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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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47A LYS* 2.7 34.8 + - - +
85A ALA 2.9 17.3 + - - +
86A GLU* 3.7 7.4 - - - +
87A VAL 3.3 0.2 - - - -
88A ASN* 1.3 76.8 - - - +
90A VAL* 1.3 62.5 + - + +
92A GLY* 3.6 1.6 + - - -
93A GLN* 3.4 30.4 + - - +
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Residues in contact with VAL 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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47A LYS* 3.9 32.8 - - + +
50A THR* 3.5 29.4 - - + +
51A HIS* 3.7 42.8 - - + +
54A PHE* 4.4 0.7 - - + -
86A GLU 3.4 11.2 + - - +
87A VAL 3.2 3.4 + - - +
89A GLU* 1.3 74.5 - - + +
91A TYR* 1.3 66.7 + - - +
93A GLN* 3.0 22.6 + - - +
94A TYR* 3.2 20.0 - - + -
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Residues in contact with TYR 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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54A PHE* 3.6 29.4 - + + -
74A ALA* 3.4 22.6 - - + +
76A VAL* 3.6 29.8 - - + -
87A VAL* 2.9 22.2 + - + +
88A ASN* 3.5 8.7 - - - +
90A VAL* 1.3 77.0 - - - +
92A GLY* 1.3 61.3 + - - +
94A TYR* 3.2 13.3 + - - +
95A PHE* 3.3 40.0 + + - -
100A PRO* 4.7 6.8 - - - +
102A ARG* 3.3 31.4 - - - +
118A ILE* 4.3 6.5 - - + -
16B PRO* 3.4 37.4 + - + -
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Residues in contact with GLY 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 ASN 2.8 16.1 + - - -
89A GLU* 4.0 3.1 - - - -
90A VAL 3.1 0.4 - - - -
91A TYR* 1.3 75.5 - - - +
93A GLN* 1.3 63.7 + - - +
94A TYR 3.2 0.2 - - - -
95A PHE 3.4 2.1 - - - +
96A ASP* 3.3 25.6 + - - +
16B PRO* 3.8 22.2 - - - -
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Residues in contact with GLN 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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51A HIS* 3.3 20.9 + - - -
89A GLU* 3.4 29.7 + - - +
90A VAL* 3.0 21.5 + - - +
92A GLY* 1.3 77.3 - - - +
94A TYR* 1.3 61.6 + - + +
96A ASP* 4.0 11.8 - - - +
503A ACY 3.1 36.2 + - + +
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Residues in contact with TYR 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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51A HIS* 2.8 30.4 + + - -
54A PHE* 3.4 58.0 - + + +
55A SER* 5.1 3.7 + - - -
58A LYS* 5.7 5.2 - - + -
68A PHE* 3.7 44.9 - + + +
69A GLU* 4.4 7.4 - - - +
90A VAL* 3.2 30.7 - - + -
91A TYR 3.2 1.5 + - - +
93A GLN* 1.3 82.2 - - + +
95A PHE* 1.3 66.0 + - + +
96A ASP* 3.4 3.6 + - - +
98A HIS* 6.0 0.2 - - - +
503A ACY 3.6 31.2 + - + -
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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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54A PHE* 3.6 22.0 - + - -
68A PHE* 3.4 48.7 - + + -
71A VAL* 3.8 15.9 - - + -
74A ALA* 5.3 2.5 - - + -
91A TYR* 3.3 53.2 + + + +
92A GLY 3.4 7.2 - - - +
94A TYR* 1.3 78.4 - - - +
96A ASP* 1.3 61.5 + - - +
98A HIS* 3.2 23.2 - + + +
99A LYS* 4.2 5.9 + - - +
100A PRO* 3.5 32.5 - - + -
118A ILE* 6.4 0.4 - - + -
120A VAL* 5.0 7.0 - - + -
16B PRO* 3.8 17.7 - - + +
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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