Contacts of the helix formed by residues 92 - 110 (chain D) in PDB entry 6EKK
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 92 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D ASP* 2.7 23.2 + - - +
90D VAL 3.3 0.6 - - - -
91D THR* 1.3 81.0 + - - +
93D ALA* 1.3 62.4 + - - +
94D GLU* 3.7 5.9 + - - +
95D SER* 2.8 48.3 + - - -
96D PHE 3.5 2.6 + - - -
130D VAL* 3.9 6.3 - - - +
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Residues in contact with ALA 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D THR 4.2 1.2 + - - -
92D SER* 1.3 72.9 + - - +
94D GLU* 1.3 59.5 + - + +
96D PHE* 3.1 7.3 + - - +
97D VAL* 3.0 30.6 + - + +
129D VAL* 3.8 24.2 - - + +
130D VAL* 4.2 11.7 - - + -
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Residues in contact with GLU 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D ASP* 4.0 5.0 - - - +
92D SER* 3.3 5.9 + - - +
93D ALA* 1.3 76.9 - - + +
95D SER* 1.3 66.0 + - - +
97D VAL* 3.4 28.2 + - + +
98D ASN* 3.2 21.8 + - - +
101D ARG* 4.5 7.6 + - - -
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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
----------------------------------------------------------
16D ASP* 3.4 21.7 + - - -
19D VAL* 3.9 16.2 - - - -
87D VAL 5.4 0.2 - - - -
88D TYR* 3.8 2.5 - - - -
89D ASP 2.9 30.4 + - - -
92D SER* 2.8 33.9 + - - -
94D GLU* 1.3 78.5 - - - +
96D PHE* 1.3 60.3 + - - +
98D ASN* 3.7 2.4 + - - +
99D VAL* 3.3 28.1 + - - +
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Residues in contact with PHE 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D TYR* 3.8 32.5 - + + -
92D SER 3.5 0.6 + - - +
93D ALA 3.1 9.7 + - - +
95D SER* 1.3 80.7 + - - +
97D VAL* 1.3 67.6 + - + +
99D VAL* 3.2 10.3 - - + +
100D LYS* 3.1 60.6 + - + +
117D LEU* 4.4 9.9 - - + -
130D VAL* 3.7 32.8 - - + -
134D ASP* 4.5 7.2 - - + -
135D ALA* 3.8 36.6 - - + -
138D PHE* 4.4 7.6 - + + -
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Residues in contact with VAL 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D ALA* 3.0 20.7 + - + +
94D GLU* 3.6 29.8 - - + +
96D PHE* 1.3 78.9 - - + +
98D ASN* 1.3 62.9 + - - +
100D LYS* 3.4 16.9 + - - +
101D ARG* 3.3 48.7 + - + +
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Residues in contact with ASN 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D ASP* 2.8 31.0 + - - +
68D GLU* 3.3 25.1 + - - +
70D PHE 4.1 2.8 + - - -
71D ARG* 4.1 6.8 - - - +
94D GLU* 3.2 13.2 + - - +
95D SER 3.8 8.5 - - - +
97D VAL* 1.3 77.9 - - - +
99D VAL* 1.3 63.2 + - - +
101D ARG* 2.4 42.9 + - - +
102D TRP* 3.0 42.1 + - + -
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Residues in contact with VAL 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D GLY* 4.9 0.2 - - - -
16D ASP 5.6 0.9 - - - +
86D VAL* 3.6 21.5 - - + -
87D VAL 3.4 27.4 - - - +
88D TYR* 4.1 3.1 - - + -
95D SER 3.3 15.0 + - - +
96D PHE* 3.2 29.1 + - + +
98D ASN* 1.3 76.4 - - + +
100D LYS* 1.3 57.9 + - + +
102D TRP* 3.6 21.9 - - + +
103D LEU* 2.9 35.0 + - + +
117D LEU* 3.8 22.7 - - + -
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Residues in contact with LYS 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D PHE* 3.1 48.8 + - + +
97D VAL* 3.6 17.0 - - - +
98D ASN 3.2 0.2 - - - -
99D VAL* 1.3 77.0 - - - +
101D ARG* 1.3 60.7 + - + +
103D LEU* 3.4 1.2 + - - -
104D HIS* 3.0 33.5 + - + -
138D PHE* 3.6 47.4 - - + -
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Residues in contact with ARG 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D ARG* 2.8 40.5 + - - +
72D THR* 4.3 12.2 - - - +
94D GLU* 4.5 6.1 + - - -
97D VAL* 3.3 35.6 + - + +
98D ASN* 2.4 36.0 + - - +
100D LYS* 1.3 78.0 - - - +
102D TRP* 1.3 64.7 + - - +
104D HIS* 3.3 9.0 + - + +
105D GLU* 3.1 23.8 + - - +
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Residues in contact with TRP 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D ILE* 3.5 32.1 - - + -
15D GLY* 3.4 37.2 - - - -
16D ASP* 3.7 16.4 - - - -
67D GLN* 3.3 31.0 - - + -
70D PHE 2.8 21.6 + - - -
71D ARG 3.4 12.4 + - - -
72D THR* 3.8 0.4 - - - -
73D ILE* 3.5 34.2 - - + +
78D TYR* 4.7 3.5 + - - +
86D VAL* 4.5 2.0 - - + -
98D ASN* 3.0 28.6 + - + -
99D VAL* 3.6 23.8 - - + +
100D LYS 3.3 0.2 - - - -
101D ARG* 1.3 75.4 - - - +
103D LEU* 1.3 58.7 + - + +
105D GLU* 3.3 7.2 + - - +
106D ILE* 2.9 34.2 + - + +
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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
----------------------------------------------------------
86D VAL* 3.8 31.2 - - + -
99D VAL 2.9 21.0 + - - +
100D LYS 3.9 3.4 - - - +
102D TRP* 1.3 73.7 - - - +
104D HIS* 1.3 61.0 + - - +
106D ILE* 3.8 9.4 - - + +
107D ASN* 3.0 27.5 + - - +
115D ARG* 4.3 20.3 + - + +
116D ILE 5.3 0.4 - - - +
117D LEU* 3.8 26.0 - - + -
138D PHE* 3.8 26.9 - - + -
142D MET* 3.5 9.2 - - + +
144D ILE* 3.9 23.8 - - + -
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Residues in contact with HIS 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D LYS* 3.0 31.0 + - + +
101D ARG* 3.6 8.7 - - - +
102D TRP 3.3 0.2 - - - -
103D LEU* 1.3 76.6 - - - +
105D GLU* 1.3 63.2 + - - +
107D ASN* 3.2 6.2 + - - +
108D GLN* 3.0 30.4 + - + +
138D PHE* 3.8 16.6 - + - -
142D MET* 3.8 26.4 - - + +
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Residues in contact with GLU 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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359B THR 4.7 6.4 - - - +
360B GLN* 4.8 3.1 + - - +
365B LYS* 4.7 6.9 + - - -
72D THR* 3.5 25.7 - - + +
73D ILE 3.3 22.2 - - - +
74D THR* 4.1 18.5 - - - +
75D SER 4.8 3.1 + - - +
78D TYR* 6.0 0.2 - - + -
101D ARG 3.1 13.4 + - - +
102D TRP 3.3 8.5 + - - +
104D HIS* 1.3 76.8 - - - +
106D ILE* 1.3 58.6 + - + +
108D GLN* 3.4 2.7 + - - +
109D ASN* 2.9 55.7 + - + +
110D CYS* 4.7 1.1 - - - -
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Residues in contact with ILE 106 (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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14D ILE* 4.7 0.7 - - + -
78D TYR* 3.5 46.0 - - + +
84D VAL* 4.9 4.3 - - + -
86D VAL* 4.7 11.4 - - + -
102D TRP 2.9 25.0 + - - +
103D LEU* 3.8 19.3 - - + +
105D GLU* 1.3 75.3 - - + +
107D ASN* 1.3 61.9 + - - +
110D CYS* 2.8 50.4 + - + +
111D ASP* 3.2 0.3 + - - -
113D VAL* 3.7 4.9 - - + -
115D ARG* 3.4 35.2 - - - +
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Residues in contact with ASN 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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103D LEU 3.0 14.7 + - - +
104D HIS* 3.3 11.5 + - - +
106D ILE* 1.3 77.8 - - - +
108D GLN* 1.3 75.8 + - - +
111D ASP* 3.5 29.6 - - - +
115D ARG* 3.9 15.4 + - - +
142D MET* 3.8 27.5 - - + +
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Residues in contact with GLN 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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104D HIS* 3.0 22.9 + - + +
105D GLU* 4.5 1.8 - - - +
106D ILE 3.2 0.2 - - - -
107D ASN* 1.3 92.5 - - - +
109D ASN* 1.3 76.8 + - - +
111D ASP* 5.7 0.2 - - - -
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Residues in contact with ASN 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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339B GLU* 5.8 0.8 + - - -
356B GLN* 5.4 2.8 - - - +
360B GLN* 3.3 40.3 + - - +
75D SER* 3.9 13.6 - - - -
105D GLU* 2.9 40.5 + - + +
106D ILE 3.3 0.2 + - - -
108D GLN* 1.3 92.5 + - - +
110D CYS* 1.3 62.6 + - - +
111D ASP 3.8 1.8 - - - -
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Residues in contact with CYS 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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75D SER* 3.7 19.5 - - - -
78D TYR* 3.6 37.9 - - + -
105D GLU* 4.7 1.1 - - - -
106D ILE* 2.8 30.5 + - - +
109D ASN* 1.3 78.7 - - - +
111D ASP* 1.3 59.8 + - - +
112D ASP* 3.0 8.0 + - - -
113D VAL* 3.1 30.3 + - + +
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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
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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) + - + + + + + -
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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