Contacts of the helix formed by residues 110 - 128 (chain B) in PDB entry 4BSX
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 PRO 110 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B ALA* 4.2 0.2 - - - +
109B CYS* 1.3 98.1 - - + +
111B ALA* 1.3 58.4 + - - +
112B SER* 3.0 16.2 - - - +
113B MSE 2.9 43.6 + - + +
114B ARG 3.8 0.7 - - - +
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Residues in contact with ALA 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ALA* 4.0 14.8 - - + +
109B CYS 3.7 1.2 + - - -
110B PRO* 1.3 69.9 - - - +
112B SER* 1.3 63.9 + - - +
113B MSE 3.1 0.9 + - - -
114B ARG* 3.3 29.2 - - - +
115B ASP* 3.3 25.8 + - - +
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Residues in contact with SER 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B PRO* 4.0 13.8 - - - +
111B ALA* 1.3 79.6 - - - +
113B MSE 1.3 73.5 + - - +
115B ASP* 3.2 13.3 + - - +
116B VAL* 3.1 32.2 + - - +
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Residues in contact with MSE 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B GLY* 5.2 5.4 - - - -
6B PRO* 4.0 28.0 - - - +
14B ILE* 6.2 0.7 - - + -
100B TYR* 3.8 26.0 - - + -
109B CYS* 4.3 4.0 - - + -
110B PRO* 2.9 31.3 + - + +
112B SER* 1.3 100.1 + - - +
114B ARG* 1.3 65.6 + - - +
116B VAL* 3.5 17.7 + - + +
117B ALA* 3.1 22.9 + - - +
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Residues in contact with ARG 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ALA 4.5 0.7 - - - +
100B TYR* 4.0 23.7 - - - +
101B HIS* 3.5 45.4 + - - +
104B ALA* 4.4 11.8 - - + +
105B GLU* 4.5 9.3 + - - -
109B CYS* 5.2 0.2 - - - -
110B PRO 3.8 2.4 - - - +
111B ALA* 3.3 32.6 - - - +
113B MSE 1.3 79.6 + - - +
115B ASP* 1.3 77.8 + - - +
117B ALA* 3.3 2.9 - - - -
118B TYR* 3.0 41.6 - - + -
143B ARG 3.3 22.7 + - - -
144B CYS* 3.7 19.7 + - - -
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Residues in contact with ASP 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B ALA* 3.5 10.6 - - - +
112B SER* 3.2 13.7 + - - +
114B ARG* 1.3 95.7 + - - +
116B VAL* 1.3 70.4 + - + +
118B TYR* 3.2 4.0 + - - +
119B GLN* 3.0 30.4 + - + +
144B CYS* 3.3 21.5 - - - +
146B TRP* 3.3 36.7 + - + -
148B ILE* 4.3 1.5 - - + +
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Residues in contact with VAL 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B PRO* 3.5 18.8 - - + -
112B SER* 3.1 15.7 + - - +
113B MSE 3.9 20.2 - - + +
115B ASP* 1.3 79.6 - - + +
117B ALA* 1.3 57.3 + - - +
119B GLN* 3.3 17.8 + - + +
120B GLU* 3.0 50.0 + - + +
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Residues in contact with ALA 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B PRO* 4.0 18.8 - - + +
93B SER 4.3 2.5 - - - +
96B VAL* 4.4 5.2 - - + -
97B ALA* 3.6 28.1 - - - +
100B TYR* 4.3 7.9 - - + -
113B MSE 3.1 18.0 + - - +
114B ARG 3.6 5.2 - - - -
115B ASP 3.2 0.2 - - - -
116B VAL* 1.3 78.0 - - - +
118B TYR* 1.3 62.8 + - - +
120B GLU* 3.4 6.8 + - - +
121B ALA* 3.0 23.2 + - - +
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Residues in contact with TYR 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B TRP* 4.5 0.4 - - - -
97B ALA* 3.6 32.8 - - + -
98B ARG* 3.7 6.2 - - - +
101B HIS* 4.4 2.2 - - + -
114B ARG* 3.0 24.8 - - + -
115B ASP 3.2 1.1 + - - +
117B ALA* 1.3 74.1 - - - +
119B GLN* 1.3 62.7 + - - +
121B ALA* 3.2 4.1 + - - +
122B VAL* 3.0 28.3 + - - +
136B LEU* 3.9 17.5 - - + -
139B GLU* 2.4 44.9 + - + +
140B ALA* 3.7 28.3 - - + -
143B ARG* 3.2 35.9 + - + -
144B CYS* 3.5 23.3 - - - -
148B ILE 3.8 8.3 - - - +
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Residues in contact with GLN 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B ASP* 3.0 18.1 + - - +
116B VAL* 3.3 25.4 + - - +
118B TYR* 1.3 75.6 - - - +
120B GLU* 1.3 55.3 + - - +
122B VAL* 2.7 28.4 + - - +
123B ARG* 2.8 28.9 + - - +
146B TRP* 4.6 7.0 - - - -
148B ILE* 3.5 44.7 + - + +
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Residues in contact with GLU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B PRO* 3.8 28.4 - - - +
93B SER* 4.5 6.3 - - - -
116B VAL* 3.0 39.1 + - + +
117B ALA* 3.8 5.4 - - - +
119B GLN* 1.3 75.3 - - - +
121B ALA* 1.3 57.9 + - - +
123B ARG* 3.4 30.9 + - - +
124B THR* 2.9 35.0 + - - +
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Residues in contact with ALA 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B SER* 3.4 34.9 - - - +
94B TRP* 4.1 7.4 - - + +
97B ALA* 4.5 1.3 - - + -
117B ALA 3.0 14.2 + - - +
118B TYR* 3.5 11.0 - - - +
119B GLN 3.0 0.4 - - - -
120B GLU* 1.3 77.2 - - - +
122B VAL* 1.3 59.4 + - - +
124B THR* 3.3 0.5 + - - -
125B LEU* 3.0 35.9 + - - +
136B LEU* 3.6 19.3 - - + -
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Residues in contact with VAL 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B TYR 3.0 18.6 + - - +
119B GLN* 2.7 11.3 + - - +
121B ALA* 1.3 76.8 - - - +
123B ARG* 1.3 58.9 + - - +
125B LEU 3.4 0.3 + - - -
126B SER* 2.9 37.9 + - - +
133B LEU* 3.7 12.6 - - + +
136B LEU* 3.7 23.8 - - + -
137B GLN* 4.5 22.9 - - + +
140B ALA* 4.5 12.8 - - + -
148B ILE* 5.1 17.7 - - + +
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Residues in contact with ARG 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B GLN* 2.8 22.4 + - - +
120B GLU* 3.5 41.8 + - - +
122B VAL* 1.3 77.5 - - - +
124B THR* 1.3 63.3 + - - +
126B SER* 3.2 6.4 + - - -
127B SER* 3.0 26.4 + - - -
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Residues in contact with THR 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B ASP* 3.1 40.1 + - - +
93B SER* 3.6 14.1 + - - +
120B GLU* 2.9 22.9 + - - +
121B ALA 3.3 1.1 + - - -
123B ARG* 1.3 73.7 - - - +
125B LEU* 1.3 61.5 + - - +
127B SER* 2.8 25.2 + - - +
128B ARG* 3.6 14.1 - - - +
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Residues in contact with LEU 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B ASP* 4.0 10.3 - - - +
93B SER* 4.3 5.2 - - - +
94B TRP* 3.9 31.9 - - + -
121B ALA* 3.0 30.4 + - + +
124B THR* 1.3 72.5 - - - +
126B SER* 1.3 60.5 + - - +
128B ARG* 3.4 22.7 + - - +
129B ASP 3.1 3.1 + - - -
130B ASP* 3.0 48.3 + - + +
132B ARG 4.0 20.4 - - - +
133B LEU* 3.7 15.3 - - + -
136B LEU* 3.7 21.8 - - + -
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Residues in contact with SER 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B VAL* 2.9 24.6 + - - +
123B ARG* 3.5 7.2 - - - -
125B LEU* 1.3 77.8 - - - +
127B SER* 1.3 58.3 + - - +
129B ASP* 2.8 21.7 + - - +
133B LEU* 3.4 26.3 - - - +
137B GLN* 5.3 0.3 + - - -
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Residues in contact with SER 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B ARG* 3.0 15.1 + - - -
124B THR* 2.8 22.9 + - - +
126B SER* 1.3 76.8 - - - +
128B ARG* 1.3 59.3 + - - +
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Residues in contact with ARG 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B ASP* 2.9 40.5 + - - +
124B THR* 3.6 18.2 + - - +
125B LEU* 3.7 24.1 - - - +
126B SER 3.0 0.2 - - - -
127B SER* 1.3 81.0 + - - +
129B ASP* 1.3 70.5 + - - +
130B ASP* 2.7 33.9 + - - +
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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
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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