Contacts of the helix formed by residues 90 - 115 (chain h) 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 h).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86h GLN 3.9 6.7 + - - +
87h LEU* 3.3 16.8 + - - +
88h ASN 3.2 2.6 - - - +
89h ASP* 1.3 77.9 - - + +
91h PRO* 1.3 64.4 - - - +
92h GLU* 3.4 1.3 - - + +
93h VAL* 4.2 19.3 - - + +
94h ARG* 3.3 12.1 + - - +
19p ASN* 5.7 6.5 - - + -
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Residues in contact with PRO 91 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88h ASN 4.7 2.4 - - - +
89h ASP 3.9 3.6 - - - -
90h LYS* 1.3 71.4 - - - +
92h GLU* 1.3 57.2 + - - +
94h ARG* 3.4 5.2 + - + +
95h SER* 2.9 29.5 + - - -
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Residues in contact with GLU 92 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90h LYS* 3.4 1.7 - - + +
91h PRO* 1.3 78.3 - - - +
93h VAL* 1.3 64.3 + - - +
95h SER* 3.1 7.6 + - - -
96h GLU* 2.9 23.4 + - - +
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Residues in contact with VAL 93 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107e ILE* 6.3 2.5 - - + -
87h LEU* 5.0 6.7 - - + +
90h LYS* 3.8 19.4 + - + +
91h PRO 3.4 0.2 - - - -
92h GLU* 1.3 77.5 - - - +
94h ARG* 1.3 58.1 + - - +
96h GLU* 3.3 7.2 + - - +
97h ILE* 2.9 30.9 + - - +
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Residues in contact with ARG 94 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87h LEU* 3.7 16.0 + - + +
88h ASN* 5.0 5.4 - - - +
90h LYS 3.3 17.7 + - - +
91h PRO* 3.7 5.8 - - + +
92h GLU 3.3 0.4 - - - -
93h VAL* 1.3 77.3 - - - +
95h SER* 1.3 57.0 + - - +
97h ILE* 3.5 5.9 + - - +
98h ASP* 2.9 30.0 + - - +
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Residues in contact with SER 95 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91h PRO 2.9 15.5 + - - -
92h GLU* 3.4 11.9 - - - -
94h ARG* 1.3 77.6 - - - +
96h GLU* 1.3 56.9 + - - +
98h ASP* 3.2 8.3 + - - +
99h SER* 2.9 27.5 + - - -
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Residues in contact with GLU 96 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92h GLU 2.9 12.5 + - - +
93h VAL* 3.7 9.4 - - - +
95h SER* 1.3 77.4 - - - +
97h ILE* 1.3 63.0 + - - +
99h SER* 3.0 9.5 + - - -
100h LEU* 3.0 23.3 + - - +
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Residues in contact with ILE 97 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104e ILE* 6.4 3.4 - - + -
107e ILE* 6.1 5.6 - - + -
93h VAL 2.9 17.6 + - - +
94h ARG* 3.9 7.0 - - - +
96h GLU* 1.3 74.6 - - - +
98h ASP* 1.3 57.9 + - - +
100h LEU* 3.4 6.5 + - - +
101h VAL* 2.9 30.9 + - - +
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Residues in contact with ASP 98 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94h ARG 2.9 18.6 + - - +
95h SER* 3.5 8.3 - - - +
96h GLU 3.2 0.2 - - - -
97h ILE* 1.3 77.1 - - - +
99h SER* 1.3 57.7 + - - +
101h VAL* 3.8 4.9 - - - +
102h SER* 2.9 29.5 + - - -
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Residues in contact with SER 99 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95h SER 2.9 14.0 + - - -
96h GLU* 3.0 12.5 + - - -
98h ASP* 1.3 75.7 - - - +
100h LEU* 1.3 62.6 + - - +
102h SER* 3.1 9.1 + - - -
103h LEU* 2.9 21.9 + - - +
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Residues in contact with LEU 100 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100e LEU* 5.0 21.9 - - + +
103e LEU* 5.8 3.8 - - + -
104e ILE* 5.3 11.9 - - + +
96h GLU 3.0 14.6 + - - +
97h ILE* 3.9 7.0 - - - +
99h SER* 1.3 74.5 - - - +
101h VAL* 1.3 63.9 + - - +
103h LEU* 3.0 10.1 + - - +
104h ILE* 3.0 23.7 + - - +
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Residues in contact with VAL 101 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97h ILE 2.9 18.3 + - - +
98h ASP* 4.0 5.8 - - - +
100h LEU* 1.3 76.2 - - - +
102h SER* 1.3 57.3 + - - +
104h ILE* 3.5 6.1 + - - +
105h THR* 2.9 31.4 + - - -
124h ILE* 4.4 23.8 - - + +
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Residues in contact with SER 102 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98h ASP 2.9 19.7 + - - -
99h SER* 3.1 8.9 + - - -
101h VAL* 1.3 78.1 - - - +
103h LEU* 1.3 57.0 + - - +
105h THR* 3.4 6.3 + - - -
106h ASP* 2.9 28.6 + - - +
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Residues in contact with LEU 103 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100e LEU* 5.8 5.6 - - + -
99h SER 2.9 12.2 + - - +
100h LEU* 3.0 11.2 + - - +
102h SER* 1.3 76.6 - - - +
104h ILE* 1.3 62.1 - - - +
106h ASP* 3.0 10.1 + - - +
107h ILE* 3.0 21.7 + - - +
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Residues in contact with ILE 104 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97e ILE* 6.4 3.1 - - + -
100e LEU* 5.5 9.0 - - + -
100h LEU 3.0 14.9 + - - +
101h VAL* 3.9 7.2 - - - +
103h LEU* 1.3 75.1 - - - +
105h THR* 1.3 58.9 + - - +
107h ILE* 3.1 7.9 + - - +
108h ILE* 2.9 30.4 + - - +
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Residues in contact with THR 105 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101h VAL 2.9 20.0 + - - -
102h SER* 3.7 6.7 - - - -
104h ILE* 1.3 76.1 - - - +
106h ASP* 1.3 57.5 + - - +
108h ILE* 4.2 4.8 - - - +
109h MET* 2.9 31.5 + - - +
124h ILE* 5.8 8.7 - - - -
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Residues in contact with ASP 106 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102h SER 2.9 14.4 + - - +
103h LEU* 3.3 11.9 - - - +
105h THR* 1.3 74.8 - - - +
107h ILE* 1.3 60.0 + - - +
109h MET* 3.3 5.9 + - - +
110h ALA* 2.9 29.6 + - - +
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Residues in contact with ILE 107 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93e VAL* 6.2 2.9 - - + +
97e ILE* 6.1 5.6 - - + -
103h LEU 3.0 11.6 + - - +
104h ILE* 3.1 9.8 + - - +
106h ASP* 1.3 76.3 - - - +
108h ILE* 1.3 64.9 + - - +
110h ALA* 3.1 7.9 + - - +
111h GLU* 3.0 22.1 + - - +
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Residues in contact with ILE 108 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130e ILE* 6.3 3.1 - - + -
133e LEU* 5.9 7.2 - - + -
104h ILE 2.9 16.0 + - - +
105h THR* 4.2 5.2 - - - +
107h ILE* 1.3 75.6 - - - +
109h MET* 1.3 58.0 + - - +
111h GLU* 3.3 9.2 + - - +
112h CYS* 2.9 27.4 + - - +
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Residues in contact with MET 109 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105h THR 2.9 21.0 + - - +
106h ASP* 3.6 6.7 - - - +
107h ILE 3.2 0.2 - - - -
108h ILE* 1.3 73.9 - - - +
110h ALA* 1.3 60.8 + - - +
112h CYS* 3.1 8.5 + - - +
113h ILE* 2.9 28.2 + - - +
27u SER* 4.8 18.7 - - - -
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Residues in contact with ALA 110 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106h ASP 2.9 13.7 + - - +
107h ILE* 3.1 10.7 + - - +
109h MET* 1.3 76.0 - - - +
111h GLU* 1.3 61.1 + - - +
113h ILE* 3.1 8.5 + - - +
114h GLU* 2.9 23.2 + - - +
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Residues in contact with GLU 111 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83e ILE* 5.3 18.9 - - + +
86e GLN* 5.3 12.7 - - + +
87e LEU* 5.7 6.5 - - + +
107h ILE 3.0 11.4 + - - +
108h ILE* 3.6 12.6 - - - +
110h ALA* 1.3 76.7 - - - +
112h CYS* 1.3 60.6 + - - +
114h GLU* 3.4 15.2 + - - +
115h ASN* 3.5 11.1 + - - +
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Residues in contact with CYS 112 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108h ILE 2.9 13.9 + - - +
109h MET* 3.1 11.4 + - - +
111h GLU* 1.3 76.1 - - - +
113h ILE* 1.3 64.0 + - - +
115h ASN* 3.3 21.9 + - - +
117h LEU 4.3 6.4 - - - +
119h ILE* 4.3 25.8 + - + +
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Residues in contact with ILE 113 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109h MET 2.9 13.4 + - - +
110h ALA* 3.1 10.5 + - - +
112h CYS* 1.3 76.3 - - - +
114h GLU* 1.3 62.5 + - - +
115h ASN 3.3 8.0 + - - +
12u HIS* 5.3 7.6 - - + +
13u SER* 5.0 16.6 - - - +
14u LYS* 4.0 17.6 + - - +
25u ARG 5.5 2.5 - - - +
26u ASN 5.7 0.4 - - - -
27u SER* 5.3 15.7 - - - +
49u VAL* 5.1 2.3 - - - +
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Residues in contact with GLU 114 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86e GLN* 6.5 1.3 - - + -
110h ALA 2.9 12.3 + - - +
111h GLU* 3.7 13.5 - - - +
112h CYS 3.2 0.6 - - - -
113h ILE* 1.3 78.3 - - - +
115h ASN* 1.3 59.5 + - - +
116h GLU 3.9 0.3 + - - -
49u VAL* 5.1 11.2 - - - +
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Residues in contact with ASN 115 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111h GLU 3.5 7.4 + - - +
112h CYS* 3.3 15.5 + - - +
113h ILE 3.2 11.3 - - - +
114h GLU* 1.3 81.8 - - - +
116h GLU* 1.3 63.8 + - - +
117h LEU* 3.4 16.4 - - + +
119h ILE* 6.1 2.0 - - + -
14u LYS* 4.6 8.0 - - - +
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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