Contacts of the helix formed by residues 90 - 115 (chain D) in PDB entry 6QXT
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 LYS 90 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D GLN 3.9 6.3 + - - +
87D LEU* 3.3 17.5 + - - +
88D ASN 3.2 2.1 - - - +
89D ASP* 1.3 78.9 - - - +
91D PRO* 1.3 64.0 - - - +
92D GLU* 3.4 2.0 - - + +
93D VAL* 4.2 19.5 - - + +
94D ARG* 3.3 11.8 + - - +
19M ASN* 6.5 1.3 - - + -
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Residues in contact with PRO 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D ASN 4.7 2.2 - - - +
89D ASP 3.9 4.0 - - - -
90D LYS* 1.3 71.2 - - - +
92D GLU* 1.3 57.6 + - - +
94D ARG* 3.4 5.8 + - + +
95D SER* 2.9 29.8 + - - -
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Residues in contact with GLU 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D LYS* 3.4 1.5 - - + +
91D PRO* 1.3 78.2 - - - +
93D VAL* 1.3 64.5 + - - +
95D SER* 3.1 8.1 + - - -
96D GLU* 2.9 23.2 + - - +
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Residues in contact with VAL 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ILE* 6.4 2.2 - - + -
87D LEU* 5.0 7.4 - - + +
90D LYS* 3.8 19.7 + - + +
91D PRO 3.4 0.4 - - - -
92D GLU* 1.3 78.1 - - - +
94D ARG* 1.3 58.6 + - - +
96D GLU* 3.3 7.9 + - - +
97D ILE* 2.9 29.6 + - - +
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Residues in contact with ARG 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D LEU* 3.8 15.8 + - + +
88D ASN* 5.0 6.1 - - - +
90D LYS 3.3 16.7 + - - +
91D PRO* 3.7 5.6 - - + +
92D GLU 3.3 0.4 - - - -
93D VAL* 1.3 79.1 - - - +
95D SER* 1.3 57.2 + - - +
97D ILE* 3.5 6.1 + - - +
98D ASP* 2.9 29.8 + - - +
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Residues in contact with SER 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D PRO 2.9 16.0 + - - -
92D GLU* 3.1 11.0 + - - -
94D ARG* 1.3 76.7 - - - +
96D GLU* 1.3 62.2 + - - +
98D ASP* 3.2 7.3 + - - +
99D SER* 2.9 22.3 + - - -
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Residues in contact with GLU 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D GLU 2.9 12.9 + - - +
93D VAL* 3.3 10.1 + - - +
95D SER* 1.3 76.4 - - - +
97D ILE* 1.3 61.8 + - - +
99D SER* 3.0 9.7 + - - -
100D LEU* 2.9 22.7 + - - +
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Residues in contact with ILE 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ILE* 6.4 2.7 - - + -
107A ILE* 6.1 4.5 - - + -
93D VAL 2.9 16.9 + - - +
94D ARG* 3.9 7.2 - - - +
96D GLU* 1.3 75.6 - - - +
98D ASP* 1.3 63.0 + - - +
100D LEU* 3.2 6.1 + - - +
101D VAL* 3.0 28.3 + - - +
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Residues in contact with ASP 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D ARG 2.9 18.7 + - - +
95D SER* 3.5 8.1 - - - +
97D ILE* 1.3 76.7 - - - +
99D SER* 1.3 49.5 + - - +
101D VAL* 5.1 2.5 - - - -
102D SER* 2.7 38.3 + - - -
56K THR* 4.4 20.0 - - - +
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Residues in contact with SER 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D SER 2.9 12.9 + - - -
96D GLU* 3.0 12.3 + - - -
98D ASP* 1.3 76.9 - - - +
100D LEU* 1.3 56.2 + - - +
102D SER* 3.2 6.3 - - - -
103D LEU* 2.9 28.4 + - - +
53K THR* 5.4 0.3 - - - -
56K THR* 6.1 0.2 - - - -
57K ALA* 6.1 6.3 - - - +
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Residues in contact with LEU 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A LEU* 5.0 23.4 - - + +
103A LEU* 5.8 4.7 - - + -
104A ILE* 5.3 11.4 - - + +
96D GLU 2.9 14.5 + - - +
97D ILE* 3.2 7.6 + - - +
99D SER* 1.3 73.6 - - - +
101D VAL* 1.3 64.6 + - - +
103D LEU* 3.0 7.9 + - - +
104D ILE* 3.0 22.2 + - - +
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Residues in contact with VAL 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D ILE 3.0 15.2 + - - +
98D ASP* 4.6 2.5 - - - +
100D LEU* 1.3 76.9 - - - +
102D SER* 1.3 56.5 + - - +
104D ILE* 3.7 8.3 - - - +
105D THR* 2.9 29.3 + - - -
124D ILE* 4.4 25.1 - - + +
125D THR 6.1 0.7 - - - +
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Residues in contact with SER 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D ASP 2.7 24.0 + - - -
99D SER* 3.2 9.6 - - - -
100D LEU 3.0 0.2 - - - -
101D VAL* 1.3 77.4 - - - +
103D LEU* 1.3 62.5 + - - +
105D THR* 3.0 9.9 + - - -
106D ASP* 2.9 19.9 + - - +
52K HIS* 4.2 6.1 - - - -
53K THR* 3.4 36.7 + - - +
56K THR* 4.5 5.2 - - - -
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Residues in contact with LEU 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D SER 2.9 14.8 + - - +
100D LEU* 3.0 8.9 + - - +
102D SER* 1.3 74.4 - - - +
104D ILE* 1.3 62.9 + - - +
106D ASP* 3.0 11.3 + - - +
107D ILE* 3.0 21.8 + - - +
53K THR* 4.3 6.6 - - - -
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Residues in contact with ILE 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ILE* 6.4 2.7 - - + -
100A LEU* 5.5 9.0 - - + -
100D LEU 3.0 12.7 + - - +
101D VAL* 3.7 12.1 - - - +
103D LEU* 1.3 76.0 - - - +
105D THR* 1.3 62.9 + - - +
107D ILE* 3.1 8.1 + - - +
108D ILE* 3.0 25.7 + - - +
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Residues in contact with THR 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D VAL 2.9 14.7 + - - -
102D SER* 3.0 11.0 + - - -
104D ILE* 1.3 75.4 - - - +
106D ASP* 1.3 57.1 + - - +
108D ILE* 4.1 4.6 - - - +
109D MET* 2.9 32.2 + - - +
124D ILE* 5.8 8.3 - - - -
52K HIS* 4.3 20.0 - - - -
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Residues in contact with ASP 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D SER 2.9 11.5 + - - +
103D LEU* 3.0 13.0 + - - +
105D THR* 1.3 77.2 - - - +
107D ILE* 1.3 62.6 + - - +
109D MET* 3.3 5.9 + - - +
110D ALA* 2.9 23.9 + - - +
51K ASN* 4.1 26.2 - - + -
52K HIS* 5.6 0.4 - - - +
53K THR* 4.8 5.6 - - - +
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Residues in contact with ILE 107 (chain D).
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* 6.3 3.6 - - + -
97A ILE* 6.3 3.6 - - + -
103D LEU 3.0 11.8 + - - +
104D ILE* 3.1 10.5 + - - +
106D ASP* 1.3 76.1 - - - +
108D ILE* 1.3 63.3 + - - +
110D ALA* 3.0 9.2 + - - +
111D GLU* 3.0 21.5 + - - +
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Residues in contact with ILE 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A ILE* 6.5 0.7 - - - -
104D ILE 3.0 15.6 + - - +
105D THR* 4.2 5.2 - - - +
107D ILE* 1.3 76.6 - - - +
109D MET* 1.3 57.9 + - - +
111D GLU* 3.3 8.2 + - - +
112D CYS* 2.9 27.5 + - - +
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Residues in contact with MET 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D THR 2.9 20.7 + - - +
106D ASP* 3.5 7.2 - - - +
108D ILE* 1.3 74.5 - - - +
110D ALA* 1.3 59.1 + - - +
112D CYS* 3.1 7.6 + - - +
113D ILE* 2.9 28.6 + - - +
51K ASN* 6.1 2.9 - - + -
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Residues in contact with ALA 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D ASP 2.9 13.3 + - - +
107D ILE* 3.0 10.5 + - - +
109D MET* 1.3 76.6 - - - +
111D GLU* 1.3 62.6 + - - +
113D ILE* 3.1 8.3 + - - +
114D GLU* 3.0 23.3 + - - +
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Residues in contact with GLU 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A ILE* 5.5 13.1 - - + +
86A GLN* 5.4 13.9 - - + +
87A LEU* 5.8 6.3 - - + +
107D ILE 3.0 11.8 + - - +
108D ILE* 3.6 11.9 - - - +
110D ALA* 1.3 76.0 - - - +
112D CYS* 1.3 61.8 + - - +
114D GLU* 3.5 15.6 + - - +
115D ASN* 3.6 10.6 + - - +
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Residues in contact with CYS 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D ILE 2.9 14.7 + - - +
109D MET* 3.1 11.4 + - - +
111D GLU* 1.3 75.0 - - - +
113D ILE* 1.3 64.4 + - - +
115D ASN* 3.2 22.0 + - - +
117D LEU 4.4 6.2 - - - +
119D ILE* 4.3 25.7 + - + +
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Residues in contact with ILE 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D MET 2.9 12.9 + - - +
110D ALA* 3.1 11.0 + - - +
112D CYS* 1.3 77.4 - - - +
114D GLU* 1.3 61.6 + - - +
115D ASN 3.3 8.3 + - - +
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Residues in contact with GLU 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D ALA 3.0 12.1 + - - +
111D GLU* 3.7 12.8 - - - +
112D CYS 3.2 0.4 - - - -
113D ILE* 1.3 78.7 - - - +
115D ASN* 1.3 59.8 + - - +
116D GLU 3.9 0.5 + - - -
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Residues in contact with ASN 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D GLU 3.6 8.5 + - - +
112D CYS* 3.2 15.9 + - - +
113D ILE 3.2 9.9 - - - +
114D GLU* 1.3 82.1 - - - +
116D GLU* 1.3 64.5 + - - +
117D LEU* 3.4 16.0 - - + +
119D ILE* 6.2 1.3 - - + -
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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) + - + + + + + -
------------------------------------------------------------
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