Contacts of the helix formed by residues 82 - 99 (chain A) in PDB entry 4QNW
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 SER 82 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A GLN 5.0 0.7 + - - -
40A VAL* 5.0 0.5 - - - +
81A TRP* 1.3 99.5 - - - +
83A GLU* 1.3 63.7 + - - +
84A PRO* 3.4 12.8 - - - +
85A GLN* 3.0 38.6 + - - +
86A ARG* 3.0 28.0 + - - +
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Residues in contact with GLU 83 (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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81A TRP 4.2 0.4 + - - -
82A SER* 1.3 70.2 - - - +
84A PRO* 1.3 72.7 - - + +
86A ARG* 3.2 25.7 + - - +
87A GLU* 3.0 26.3 + - - +
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Residues in contact with PRO 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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40A VAL* 3.9 20.2 - - + +
82A SER* 3.4 13.9 - - - +
83A GLU* 1.3 93.0 - - + +
85A GLN* 1.3 62.5 + - - +
87A GLU* 3.5 16.2 + - - +
88A ALA* 3.2 22.0 + - - +
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Residues in contact with GLN 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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38A GLN 2.9 21.8 + - - +
39A GLY* 3.3 26.2 + - - +
40A VAL* 3.8 13.0 - - + +
41A PRO* 4.7 0.7 - - - -
79A GLY* 3.1 23.6 - - - +
80A ILE* 4.2 1.6 - - - -
81A TRP* 3.0 56.4 + - - -
82A SER* 3.0 30.5 + - - +
84A PRO* 1.3 77.3 - - - +
86A ARG* 1.3 57.7 + - - +
88A ALA* 3.2 4.2 + - - +
89A TRP* 2.9 35.0 + - - -
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Residues in contact with ARG 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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80A ILE* 3.8 25.8 - - + +
81A TRP 4.2 4.9 + - - -
82A SER 3.0 24.8 + - - +
83A GLU* 3.7 26.7 + - - +
85A GLN* 1.3 76.0 - - - +
87A GLU* 1.3 58.4 + - - +
89A TRP* 3.4 6.7 + - - +
90A ARG* 2.9 29.3 + - - +
161A ASN* 3.8 41.2 + - + +
164A ASN* 4.4 23.2 - - - +
165A ALA* 3.8 9.2 - - + +
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Residues in contact with GLU 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 GLU 3.0 14.6 + - - +
84A PRO* 4.0 15.7 - - - +
86A ARG* 1.3 75.1 - - - +
88A ALA* 1.3 66.1 + - - +
90A ARG* 3.3 20.0 + - - +
91A GLU* 3.2 21.3 + - - +
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Residues in contact with ALA 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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40A VAL* 3.5 31.9 - - + -
41A PRO* 3.8 18.4 - - + +
84A PRO 3.2 7.9 + - - +
85A GLN 3.2 6.5 + - - +
87A GLU* 1.3 76.5 - - - +
89A TRP* 1.3 62.6 + - - +
91A GLU* 3.2 14.8 + - - +
92A ILE* 3.1 26.6 + - + +
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Residues in contact with TRP 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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41A PRO* 3.7 17.1 - - + +
45A VAL* 5.3 0.4 - - + -
49A TYR* 4.3 5.8 - + - -
62A THR* 3.7 33.7 - - + -
63A GLU* 4.1 17.9 - - - -
65A THR* 3.5 24.7 - - + +
78A PRO* 3.6 17.5 - - + -
79A GLY 3.0 26.4 + - - -
80A ILE* 3.6 22.0 - - + -
85A GLN 2.9 25.0 + - - +
86A ARG 3.8 3.6 - - - +
88A ALA* 1.3 73.8 - - - +
90A ARG* 1.3 67.3 + - - +
91A GLU 3.1 0.2 + - - -
92A ILE* 3.2 31.6 + - + +
93A VAL* 2.9 28.0 + - - +
105A CYS* 5.1 0.7 - - - -
165A ALA* 4.4 1.8 - - + -
167A PHE* 3.5 28.5 - + + -
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Residues in contact with ARG 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ARG 2.9 18.1 + - - +
87A GLU* 3.3 17.6 + - - +
89A TRP* 1.3 74.9 - - - +
91A GLU* 1.3 69.1 - - - +
93A VAL* 3.4 1.4 + - - +
94A SER* 2.8 56.4 + - - +
164A ASN 5.3 2.2 - - - +
165A ALA* 3.5 30.6 - - + +
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Residues in contact with GLU 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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43A PRO* 5.0 7.8 - - - +
46A GLN* 3.2 32.9 - - + +
87A GLU 3.2 9.4 + - - +
88A ALA* 3.5 14.1 - - - +
89A TRP 3.1 0.4 - - - -
90A ARG* 1.3 90.3 - - - +
92A ILE* 1.3 66.1 + - - +
94A SER* 3.4 7.6 + - - -
95A ARG* 3.1 22.7 + - - +
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Residues in contact with ILE 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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41A PRO* 3.6 21.1 - - + -
42A LEU 5.4 0.7 - - - +
45A VAL* 3.6 24.2 - - + -
46A GLN* 3.8 28.0 - - + +
49A TYR* 3.7 32.9 - - + +
88A ALA* 3.1 16.9 + - + +
89A TRP* 3.5 30.7 - - + +
91A GLU* 1.3 76.8 - - + +
93A VAL* 1.3 63.4 + - + +
95A ARG* 3.1 6.1 + - - +
96A VAL* 3.1 21.7 + - - +
103A ILE* 4.3 9.6 - - + -
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Residues in contact with VAL 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 TRP 2.9 24.5 + - - +
90A ARG 3.8 2.9 - - - +
92A ILE* 1.3 74.5 - - + +
94A SER* 1.4 59.6 + - - +
96A VAL* 3.2 3.5 + - - +
97A HIS* 2.9 57.8 + - + +
103A ILE* 4.0 14.4 - - + -
165A ALA 3.8 8.7 - - - +
166A GLY* 3.5 19.1 - - - +
167A PHE* 3.5 45.3 - - + +
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Residues in contact with SER 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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90A ARG* 2.8 40.5 + - - +
91A GLU* 3.6 7.2 - - - -
93A VAL* 1.4 77.5 - - - +
95A ARG* 1.3 56.1 + - - +
97A HIS* 3.3 6.4 + - - +
98A SER* 2.8 31.1 + - - -
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Residues in contact with ARG 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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46A GLN* 3.6 42.1 + - + +
47A GLU* 5.5 3.4 - - - +
50A GLY* 4.0 13.2 - - - -
91A GLU 3.1 13.8 + - - +
92A ILE 3.1 8.7 + - - +
94A SER* 1.3 70.4 - - - +
96A VAL* 1.3 65.7 + - + +
98A SER* 2.7 36.9 + - - -
99A LYS* 3.3 40.3 + - - +
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Residues in contact with VAL 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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49A TYR* 3.9 32.8 - - + +
50A GLY 4.8 0.4 - - - +
53A ALA* 4.4 6.7 - - + -
60A LEU* 3.9 13.7 - - + -
92A ILE 3.1 13.8 + - - +
93A VAL 3.2 7.2 + - - +
95A ARG* 1.3 75.6 - - - +
97A HIS* 1.3 61.8 + - + +
99A LYS* 3.1 13.0 + - - +
101A CYS* 3.2 43.0 + - + +
102A PHE 3.9 15.5 - - - +
103A ILE* 4.0 20.2 - - + -
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Residues in contact with HIS 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 VAL* 2.9 32.5 + - + +
94A SER* 3.8 5.9 + - - +
96A VAL* 1.3 77.1 - - + +
98A SER* 1.3 67.6 + - - +
100A LYS* 3.0 21.7 + - - +
101A CYS 3.3 22.9 - - - -
102A PHE* 5.4 1.1 - + - -
103A ILE* 4.3 1.4 - - - +
166A GLY* 3.0 29.6 - - - -
168A ASP* 2.7 30.5 + - - -
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Residues in contact with SER 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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94A SER 2.8 15.2 + - - -
95A ARG* 2.7 38.8 + - - -
97A HIS* 1.3 78.5 - - - +
99A LYS* 1.4 57.8 + - - +
100A LYS* 3.3 11.9 + - - +
402A SO4 4.3 7.1 + - - -
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Residues in contact with LYS 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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50A GLY* 2.8 32.4 + - - +
51A GLN* 4.4 6.7 + - - +
53A ALA* 3.3 31.8 + - + +
54A SER* 4.7 5.9 - - - +
56A PRO* 3.9 12.0 - - - +
95A ARG* 3.3 35.8 + - - +
96A VAL 3.1 7.9 + - - +
97A HIS 3.0 1.2 - - - -
98A SER* 1.4 86.5 + - - +
100A LYS* 1.3 71.4 + - - +
101A CYS* 3.2 10.1 + - - -
364A PHE* 5.3 4.6 - - - -
368A TYR* 4.9 6.6 + - - -
402A SO4 5.4 0.9 - - - -
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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