Contacts of the helix formed by residues 104 - 125 (chain I) in PDB entry 4DHJ
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 ASP 104 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100I ILE* 2.9 16.1 + - + +
101I MET* 3.2 10.2 - - - +
103I LYS* 1.3 78.9 - - - +
105I ARG* 1.3 64.3 + - - +
106I ALA* 3.0 22.7 + - - +
107I ARG* 3.3 29.7 + - + +
108I LEU 3.1 17.3 + - - -
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Residues in contact with ARG 105 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101I MET 4.1 2.4 + - - -
102I LEU 5.5 0.2 - - - -
103I LYS 4.0 2.4 + - - -
104I ASP* 1.3 74.4 + - - +
106I ALA* 1.3 57.4 + - - +
108I LEU* 3.2 13.6 - - + +
109I GLU* 3.0 35.9 + - - +
146I ILE 5.2 0.6 + - - -
147I HIS* 2.8 65.0 + - - +
148I SER* 5.1 1.0 - - - +
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Residues in contact with ALA 106 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104I ASP* 3.0 11.5 + - - +
105I ARG* 1.3 76.4 - - - +
107I ARG* 1.3 65.3 + - - +
109I GLU* 3.3 16.7 + - - +
110I LYS* 3.0 38.5 + - - +
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Residues in contact with ARG 107 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97I LEU* 4.8 6.9 - - - +
100I ILE* 4.2 25.7 - - + +
101I MET* 4.3 7.0 - - + -
104I ASP* 3.3 32.8 + - + +
106I ALA* 1.3 76.2 - - - +
108I LEU* 1.3 53.0 + - - +
110I LYS* 3.0 13.1 + - - +
111I PHE* 2.8 38.3 + - - +
225I ALA 5.0 1.8 + - - -
226I GLY 3.8 16.8 + - - -
227I THR* 4.5 3.8 + - - -
258I GLU* 2.5 44.4 + - - -
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Residues in contact with LEU 108 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101I MET* 3.8 36.5 - - + +
104I ASP 3.1 12.6 + - - +
105I ARG* 3.2 15.7 - - + +
107I ARG* 1.3 74.8 - - - +
109I GLU* 1.3 57.9 + - - +
111I PHE* 3.1 3.6 + - - +
112I ILE* 3.0 37.7 + - + +
143I LEU* 3.6 28.5 - - + +
146I ILE* 4.0 15.5 - - + -
147I HIS* 3.5 38.8 - - + +
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Residues in contact with GLU 109 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105I ARG* 3.0 23.8 + - - +
106I ALA* 3.5 19.1 - - - +
108I LEU* 1.3 74.7 - - - +
110I LYS* 1.3 68.0 + - + +
112I ILE* 3.3 12.2 + - + +
113I ALA* 3.2 20.8 + - - +
147I HIS* 3.0 36.6 - - + +
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Residues in contact with LYS 110 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106I ALA* 3.0 28.9 + - - +
107I ARG* 3.0 18.1 + - - +
109I GLU* 1.3 80.1 - - + +
111I PHE* 1.3 58.2 + - - +
113I ALA* 3.3 8.4 + - + +
114I SER* 3.0 29.6 + - - -
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Residues in contact with PHE 111 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97I LEU* 3.9 28.3 - - + -
101I MET* 3.5 35.0 - - + -
107I ARG* 2.8 14.5 + - - +
108I LEU 3.5 1.3 - - - +
110I LYS* 1.3 74.6 - - - +
112I ILE* 1.3 58.1 + - - +
114I SER* 3.6 10.9 + - - -
115I SER* 2.7 43.0 + - - -
118I TRP* 6.5 1.1 - + - -
139I PHE* 3.5 27.6 - + - -
143I LEU* 3.6 21.1 - - + -
172I PHE* 4.7 4.7 - + - -
173I PHE* 4.2 8.5 - + - -
176I ILE* 5.3 3.4 - - + -
225I ALA* 3.8 29.8 - - + -
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Residues in contact with ILE 112 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108I LEU* 3.0 35.0 + - + +
109I GLU* 3.6 11.0 - - + +
110I LYS 3.3 0.4 - - - -
111I PHE* 1.3 78.5 - - - +
113I ALA* 1.3 62.9 + - - +
115I SER* 3.7 3.5 - - - -
116I ARG* 3.1 41.0 + - - +
140I ILE* 4.3 9.3 - - + +
143I LEU* 3.8 35.0 - - + +
144I GLU* 3.4 34.1 - - - +
147I HIS* 4.2 13.2 - - + -
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Residues in contact with ALA 113 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109I GLU 3.2 12.5 + - - +
110I LYS* 3.3 11.2 + - + +
112I ILE* 1.3 77.3 - - - +
114I SER* 1.3 62.6 + - - +
116I ARG* 3.2 13.2 + - - +
117I ASP* 3.1 26.4 + - - +
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Residues in contact with SER 114 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110I LYS 3.0 18.3 + - - -
111I PHE* 3.6 17.3 + - - -
113I ALA* 1.3 75.5 - - - +
115I SER* 1.3 61.6 + - - +
117I ASP* 3.4 13.2 + - - +
118I TRP* 3.0 41.0 + - - -
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Residues in contact with SER 115 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111I PHE* 2.7 30.4 + - - -
112I ILE* 3.7 5.6 - - - -
114I SER* 1.3 74.9 + - - +
116I ARG* 1.3 64.8 + - - +
118I TRP* 3.2 13.0 + - - +
119I THR* 3.0 26.7 + - - +
139I PHE* 3.6 21.5 - - - -
140I ILE* 3.8 19.9 - - - +
143I LEU* 5.0 0.7 - - - -
172I PHE* 3.7 15.9 - - - -
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Residues in contact with ARG 116 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112I ILE* 3.1 25.5 + - - +
113I ALA* 3.3 13.4 - - - +
115I SER* 1.3 77.4 - - - +
117I ASP* 1.3 62.6 + - - +
119I THR* 3.3 25.3 + - - -
120I ARG* 3.7 22.8 + - - +
140I ILE* 3.7 31.9 - - + +
144I GLU* 3.1 30.1 + - - +
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Residues in contact with ASP 117 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113I ALA* 3.1 16.8 + - - +
114I SER* 3.6 14.3 - - - +
115I SER 3.3 0.2 - - - -
116I ARG* 1.3 75.7 - - - +
118I TRP* 1.3 62.3 + - - +
120I ARG* 2.6 41.6 + - - +
121I THR* 3.1 29.2 + - + +
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Residues in contact with TRP 118 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111I PHE* 6.5 0.9 - + - -
114I SER* 3.0 34.8 + - - -
115I SER* 3.4 13.5 - - - +
117I ASP* 1.3 72.2 - - - +
119I THR* 1.3 67.9 + - - +
121I THR* 3.0 33.9 + - + -
122I LEU* 2.9 29.6 + - + +
172I PHE* 4.3 9.2 - + + -
176I ILE* 3.8 35.8 - - + +
179I ALA* 3.8 26.2 - - + -
180I PHE* 4.2 26.7 - + + -
183I GLN* 4.3 18.4 - - - -
224I ALA* 3.9 35.4 + - + -
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Residues in contact with THR 119 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115I SER 3.0 17.9 - - - +
116I ARG* 3.4 10.2 + - - +
117I ASP 3.3 0.2 - - - -
118I TRP* 1.3 76.4 - - - +
120I ARG* 1.3 64.5 + - - +
122I LEU* 3.4 15.8 - - - +
123I VAL* 3.5 13.1 + - - +
133I THR* 4.9 16.9 + - - +
136I CYS* 3.3 40.8 - - + -
137I ASP* 6.0 0.2 - - - -
140I ILE* 3.6 14.6 - - + -
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Residues in contact with ARG 120 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116I ARG* 3.7 27.1 + - - +
117I ASP* 2.6 42.8 + - - +
118I TRP 3.1 0.4 - - - -
119I THR* 1.3 82.2 + - - +
121I THR* 1.3 66.7 + - + +
122I LEU 3.3 0.2 - - - -
123I VAL* 3.3 10.7 + - + +
124I GLU* 3.2 25.1 + - - +
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Residues in contact with THR 121 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117I ASP* 3.1 23.1 + - + +
118I TRP* 3.0 33.6 + - + -
120I ARG* 1.3 76.3 - - + +
122I LEU* 1.3 66.5 + - - +
124I GLU* 3.1 18.6 + - - +
125I LEU* 2.9 36.4 + - - +
179I ALA* 4.7 0.5 - - - +
183I GLN* 4.2 19.3 + - - +
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Residues in contact with LEU 122 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118I TRP* 2.9 21.4 + - + +
119I THR* 3.4 7.2 - - - +
120I ARG 3.3 0.2 - - - -
121I THR* 1.3 76.9 + - - +
123I VAL* 1.3 64.1 - - + +
125I LEU 3.4 1.9 + - - -
127I PHE* 3.1 50.4 + - + +
132I CYS* 3.9 22.7 - - + +
133I THR 5.1 0.2 - - - +
136I CYS* 3.4 31.9 - - - -
175I LEU* 4.1 27.6 - - + +
176I ILE* 4.8 4.5 - - + +
179I ALA* 3.5 30.5 - - + -
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Residues in contact with VAL 123 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119I THR 3.5 13.4 + - - +
120I ARG* 3.3 13.3 + - + +
121I THR 3.1 0.8 - - - -
122I LEU* 1.3 77.1 - - + +
124I GLU* 1.3 59.3 + - + +
126I GLY* 2.9 21.3 + - - -
127I PHE 4.2 6.0 + - - +
129I ASP* 3.6 36.3 - - - +
133I THR* 4.3 9.4 - - - +
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Residues in contact with GLU 124 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120I ARG* 3.2 11.6 + - - +
121I THR* 3.1 30.2 + - - +
123I VAL* 1.3 81.1 - - + +
125I LEU* 1.3 63.7 + - + +
126I GLY 3.3 1.3 + - - -
183I GLN* 5.2 4.5 + - - -
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Residues in contact with LEU 125 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121I THR* 2.9 34.2 + - - +
123I VAL 3.2 0.4 - - - -
124I GLU* 1.3 82.8 - - + +
126I GLY* 1.3 60.9 + - - +
127I PHE* 3.4 18.4 + - + -
179I ALA* 3.6 35.9 - - + +
182I LYS* 4.5 17.7 + - + +
183I GLN* 4.2 30.1 - - + +
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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) + - + + + + + -
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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