Contacts of the helix formed by residues 90 - 115 (chain f) 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 f).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86f GLN 3.9 5.7 + - - +
87f LEU* 3.3 17.7 + - - +
88f ASN 3.2 2.4 - - - +
89f ASP* 1.3 78.0 - - - +
91f PRO* 1.3 65.2 - - - +
92f GLU* 3.4 1.1 - - + +
93f VAL* 4.2 20.2 - - + +
94f ARG* 3.3 11.4 + - - +
19j ASN* 5.6 11.0 - - + +
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Residues in contact with PRO 91 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88f ASN 4.7 2.2 - - - +
89f ASP 3.9 3.6 - - - -
90f LYS* 1.3 72.2 - - - +
92f GLU* 1.3 57.1 + - - +
94f ARG* 3.4 5.3 + - + +
95f SER* 2.9 30.1 + - - -
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Residues in contact with GLU 92 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90f LYS* 3.4 1.7 - - + +
91f PRO* 1.3 78.4 - - - +
93f VAL* 1.3 64.6 + - - +
95f SER* 3.1 8.4 + - - -
96f GLU* 2.9 22.9 + - - +
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Residues in contact with VAL 93 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87f LEU* 5.0 7.2 - - + +
90f LYS* 3.8 19.6 + - + +
91f PRO 3.4 0.2 - - - -
92f GLU* 1.3 78.4 - - - +
94f ARG* 1.3 57.0 + - - +
96f GLU* 3.3 6.5 + - - +
97f ILE* 2.9 30.2 + - - +
107g ILE* 6.4 2.0 - - + -
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Residues in contact with ARG 94 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87f LEU* 3.7 16.4 + - + +
88f ASN* 5.0 5.6 - - - +
90f LYS 3.3 17.1 + - - +
91f PRO* 3.7 6.3 - - + +
92f GLU 3.3 0.6 - - - -
93f VAL* 1.3 77.9 - - - +
95f SER* 1.3 57.8 + - - +
97f ILE* 3.5 6.2 + - - +
98f ASP* 2.9 29.1 + - - +
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Residues in contact with SER 95 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91f PRO 2.9 15.3 + - - -
92f GLU* 3.1 11.4 + - - -
94f ARG* 1.3 76.4 - - - +
96f GLU* 1.3 57.8 + - - +
98f ASP* 3.2 8.3 + - - +
99f SER* 2.9 27.8 + - - -
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Residues in contact with GLU 96 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92f GLU 2.9 12.5 + - - +
93f VAL* 3.7 9.6 - - - +
95f SER* 1.3 77.4 - - - +
97f ILE* 1.3 63.1 + - - +
99f SER* 3.0 9.3 + - - -
100f LEU* 3.0 23.1 + - - +
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Residues in contact with ILE 97 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93f VAL 2.9 17.2 + - - +
94f ARG* 3.8 6.5 - - - +
96f GLU* 1.3 76.2 - - - +
98f ASP* 1.3 57.5 + - - +
100f LEU* 3.4 6.1 + - - +
101f VAL* 2.9 31.6 + - - +
104g ILE* 6.4 2.9 - - + -
107g ILE* 6.1 5.6 - - + -
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Residues in contact with ASP 98 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94f ARG 2.9 18.7 + - - +
95f SER* 3.5 7.6 - - - +
97f ILE* 1.3 78.1 - - - +
99f SER* 1.3 56.2 + - - +
101f VAL* 3.9 4.7 - - - +
102f SER* 2.9 30.2 + - - -
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Residues in contact with SER 99 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95f SER 2.9 12.9 + - - -
96f GLU* 3.0 12.5 + - - -
98f ASP* 1.3 77.6 - - - +
100f LEU* 1.3 63.3 + - - +
102f SER* 3.1 8.3 + - - -
103f LEU* 2.9 21.7 + - - +
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Residues in contact with LEU 100 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96f GLU 3.0 14.7 + - - +
97f ILE* 3.9 6.1 - - - +
99f SER* 1.3 74.9 - - - +
101f VAL* 1.3 63.6 + - - +
103f LEU* 3.0 10.0 + - - +
104f ILE* 3.0 23.1 + - - +
100g LEU* 5.0 21.6 - - + +
103g LEU* 5.8 4.3 - - + -
104g ILE* 5.2 12.1 - - + +
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Residues in contact with VAL 101 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97f ILE 2.9 18.4 + - - +
98f ASP* 4.0 5.8 - - - +
100f LEU* 1.3 76.6 - - - +
102f SER* 1.3 58.0 + - - +
104f ILE* 3.5 6.8 + - - +
105f THR* 2.9 30.9 + - - -
124f ILE* 4.4 23.8 - - + +
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Residues in contact with SER 102 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98f ASP 2.9 20.2 + - - -
99f SER* 3.1 8.7 + - - -
101f VAL* 1.3 77.3 - - - +
103f LEU* 1.3 56.9 + - - +
105f THR* 3.4 6.8 + - - -
106f ASP* 2.9 28.1 + - - +
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Residues in contact with LEU 103 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99f SER 2.9 12.2 + - - +
100f LEU* 3.0 11.4 + - - +
102f SER* 1.3 76.0 - - - +
104f ILE* 1.3 63.0 - - - +
106f ASP* 3.0 9.5 + - - +
107f ILE* 3.0 21.7 + - - +
100g LEU* 5.7 5.6 - - + -
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Residues in contact with ILE 104 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100f LEU 3.0 14.1 + - - +
101f VAL* 3.9 6.7 - - - +
103f LEU* 1.3 75.9 - - - +
105f THR* 1.3 57.5 + - - +
107f ILE* 3.1 7.5 + - - +
108f ILE* 2.9 30.9 + - - +
97g ILE* 6.4 2.7 - - + -
100g LEU* 5.5 9.6 - - + -
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Residues in contact with THR 105 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101f VAL 2.9 18.8 + - - -
102f SER* 3.7 7.0 - - - -
104f ILE* 1.3 76.2 - - - +
106f ASP* 1.3 58.0 + - - +
108f ILE* 4.2 4.6 - - - +
109f MET* 2.9 31.8 + - - +
124f ILE* 5.8 9.2 - - - -
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Residues in contact with ASP 106 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102f SER 2.9 14.9 + - - +
103f LEU* 3.0 12.1 + - - +
105f THR* 1.3 74.8 - - - +
107f ILE* 1.3 59.1 + - - +
109f MET* 3.3 5.7 + - - +
110f ALA* 2.9 29.6 + - - +
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Residues in contact with ILE 107 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103f LEU 3.0 12.2 + - - +
104f ILE* 3.1 10.7 + - - +
106f ASP* 1.3 76.4 - - - +
108f ILE* 1.3 64.2 + - - +
110f ALA* 3.1 8.7 + - - +
111f GLU* 3.0 21.5 + - - +
93g VAL* 6.2 3.4 - - + +
97g ILE* 6.0 5.6 - - + -
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Residues in contact with ILE 108 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104f ILE 2.9 16.1 + - - +
105f THR* 4.2 5.2 - - - +
107f ILE* 1.3 77.0 - - - +
109f MET* 1.3 57.3 + - - +
111f GLU* 3.3 8.4 + - - +
112f CYS* 2.9 27.9 + - - +
130g ILE* 6.4 2.9 - - + -
133g LEU* 5.9 7.4 - - + -
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Residues in contact with MET 109 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27Y SER* 5.1 17.1 - - - -
105f THR 2.9 20.8 + - - +
106f ASP* 3.6 6.5 - - - +
107f ILE 3.2 0.2 - - - -
108f ILE* 1.3 75.6 - - - +
110f ALA* 1.3 59.9 + - - +
112f CYS* 3.1 8.2 + - - +
113f ILE* 2.9 27.7 + - - +
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Residues in contact with ALA 110 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106f ASP 2.9 13.6 + - - +
107f ILE* 3.1 10.7 + - - +
109f MET* 1.3 75.7 - - - +
111f GLU* 1.3 61.9 + - - +
113f ILE* 3.1 9.0 + - - +
114f GLU* 2.9 22.9 + - - +
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Residues in contact with GLU 111 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107f ILE 3.0 13.5 + - - +
108f ILE* 3.6 11.2 - - - +
110f ALA* 1.3 77.3 - - - +
112f CYS* 1.3 61.0 + - - +
114f GLU* 3.4 15.4 + - - +
115f ASN* 3.5 11.6 + - - +
83g ILE* 5.4 18.5 - - + +
86g GLN* 5.4 12.8 - - + +
87g LEU* 5.7 6.3 - - + +
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Residues in contact with CYS 112 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108f ILE 2.9 14.9 + - - +
109f MET* 3.1 11.4 + - - +
111f GLU* 1.3 74.1 - - - +
113f ILE* 1.3 64.6 + - - +
115f ASN* 3.3 21.5 + - - +
117f LEU 4.3 6.6 - - - +
119f ILE* 4.3 25.1 + - + +
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Residues in contact with ILE 113 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12Y HIS* 5.6 7.0 - - + +
13Y SER* 5.2 14.3 - - - +
14Y LYS* 4.2 17.0 + - - +
25Y ARG 5.7 2.7 - - - +
26Y ASN 5.8 0.4 - - - -
27Y SER* 5.3 16.8 - - - +
49Y VAL* 5.4 2.3 - - - +
109f MET 2.9 13.6 + - - +
110f ALA* 3.6 10.8 - - - +
112f CYS* 1.3 76.6 - - - +
114f GLU* 1.3 62.4 + - - +
115f ASN 3.3 8.5 + - - +
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Residues in contact with GLU 114 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110f ALA 2.9 13.0 + - - +
111f GLU* 3.6 12.8 - - - +
112f CYS 3.2 0.2 - - - -
113f ILE* 1.3 76.8 - - - +
115f ASN* 1.3 60.5 + - - +
116f GLU 3.9 0.2 + - - -
86g GLN* 6.5 1.3 - - + -
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Residues in contact with ASN 115 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14Y LYS* 4.8 7.4 - - - +
111f GLU 3.5 8.5 + - - +
112f CYS* 3.3 15.9 + - - +
113f ILE 3.2 10.4 - - - +
114f GLU* 1.3 82.0 - - - +
116f GLU* 1.3 66.1 + - - +
117f LEU* 3.4 15.8 - - + +
119f ILE* 6.1 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