Contacts of the helix formed by residues 113 - 132 (chain B) in PDB entry 4WLU
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 LEU 113 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B VAL* 3.4 20.9 - - + +
103B PRO 3.5 22.2 - - - +
104B ARG* 3.7 31.0 - - + +
108B MET* 4.5 7.6 - - - -
109B THR 4.3 1.1 - - - +
110B ARG* 3.4 15.3 - - - +
111B ASP 3.0 1.2 + - - -
112B ASP* 1.3 76.4 - - - +
114B PHE* 1.3 64.8 + - - +
115B ASN 3.2 2.9 + - - -
116B THR* 3.3 5.3 + - - -
117B ASN* 3.1 32.5 + - - +
142B ASN* 4.1 12.6 - - + +
143B PRO* 4.4 2.0 - - - -
401B LMR 5.0 0.2 - - - +
402B NAD 3.7 16.6 - - - +
108D MET* 4.1 20.9 - - + -
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Residues in contact with PHE 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B ASP* 2.9 17.6 + - - +
112B ASP 3.3 1.0 - - - -
113B LEU* 1.3 77.0 - - - +
115B ASN* 1.3 75.1 + - - +
118B ALA* 2.8 51.8 + - + +
143B PRO* 4.0 19.4 - - + +
146B SER* 3.6 31.4 - - - -
147B THR* 6.1 0.4 - - + -
150B ILE* 4.2 7.4 - - + -
329B LYS* 3.7 48.0 - - + +
330B GLY* 4.2 4.7 - - - -
333B PHE* 3.7 34.3 - + + -
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Residues in contact with ASN 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ASP 4.6 1.4 + - - -
113B LEU 3.3 1.2 - - - -
114B PHE* 1.3 92.2 - - - +
116B THR* 1.3 59.1 + - - +
118B ALA* 4.7 1.8 - - - -
119B THR* 4.0 12.4 + - - -
329B LYS* 5.8 0.3 - - - -
333B PHE* 5.8 1.4 - - - -
107D GLY* 3.4 33.8 - - - +
108D MET* 4.0 1.8 - - + -
109D THR* 4.2 13.4 - - - +
112D ASP* 2.7 36.7 + - - +
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Residues in contact with THR 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B VAL* 4.1 21.3 - - + -
113B LEU 3.3 5.2 + - - -
114B PHE 3.2 0.4 - - - -
115B ASN* 1.3 78.9 - - - +
117B ASN* 1.3 70.8 + - - +
118B ALA 3.4 0.4 - - - -
119B THR* 3.5 8.2 + - - -
120B ILE* 3.3 38.4 + - + +
105D LYS* 3.8 7.1 + - + +
106D PRO* 2.7 28.9 + - + +
107D GLY* 4.3 0.2 - - - -
108D MET* 3.1 26.9 - - - +
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Residues in contact with ASN 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B GLY* 3.3 10.0 - - - -
102B VAL* 2.8 32.9 + - - +
113B LEU* 3.1 19.4 + - - +
114B PHE 4.5 0.2 - - - +
116B THR* 1.3 83.6 - - - +
118B ALA* 1.3 57.2 + - - +
120B ILE* 3.7 5.3 - - - +
121B VAL* 2.7 38.8 + - - +
141B ALA* 4.9 5.4 - - + -
142B ASN 2.8 30.8 + - - +
143B PRO* 4.9 0.4 - - + -
147B THR* 4.9 3.6 - - + -
402B NAD 3.1 23.2 + - - -
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Residues in contact with ALA 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B PHE* 2.8 40.6 + - + +
115B ASN* 5.1 0.9 - - - -
117B ASN* 1.3 70.7 - - - +
119B THR* 1.3 58.3 + - - +
121B VAL* 3.9 2.2 - - - +
122B ALA* 2.9 31.9 + - - +
147B THR* 5.0 3.2 - - - +
150B ILE* 3.6 27.3 - - + +
333B PHE* 3.6 23.4 - - + -
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Residues in contact with THR 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 ASN 4.0 11.0 + - - -
116B THR* 3.5 9.3 + - - -
117B ASN 3.3 0.2 - - - -
118B ALA* 1.3 74.7 - - - +
120B ILE* 1.3 59.4 + - + +
122B ALA* 3.8 2.8 - - + +
123B THR* 2.7 46.1 + - - +
333B PHE* 3.5 22.1 - - + -
337B LEU* 5.9 4.9 - - + -
107D GLY* 5.7 1.6 - - - -
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Residues in contact with ILE 120 (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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100B ALA* 3.6 24.7 - - + +
101B GLY* 3.9 8.3 - - - -
102B VAL* 5.2 0.9 - - + -
116B THR* 3.3 37.2 + - + +
117B ASN* 3.2 18.1 + - - +
119B THR* 1.3 78.0 - - + +
121B VAL* 1.3 63.2 + - - +
123B THR* 3.2 5.3 + - - -
124B LEU* 3.0 46.4 + - + +
402B NAD 3.7 37.9 - - + +
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Residues in contact with VAL 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ILE* 5.2 6.3 - - + -
100B ALA 4.8 3.4 - - - +
117B ASN 2.7 23.4 + - - +
118B ALA 3.9 2.9 - - - +
120B ILE* 1.3 72.3 - - + +
122B ALA* 1.3 52.1 + - - +
124B LEU* 4.8 3.6 - - - -
125B THR* 2.6 45.6 + - + +
139B VAL* 4.6 7.6 - - + -
141B ALA* 3.7 30.1 - - + -
147B THR* 3.7 28.7 - - + +
150B ILE* 4.4 8.3 - - + -
151B THR* 3.4 25.6 - - - +
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Residues in contact with ALA 122 (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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118B ALA 2.9 18.8 + - - +
119B THR* 3.8 4.9 - - + +
121B VAL* 1.3 77.0 - - - +
123B THR* 1.3 61.9 + - - +
125B THR* 3.5 5.4 + - - -
126B ALA* 3.1 25.8 + - - +
150B ILE* 3.9 13.2 - - + +
154B VAL* 4.0 8.5 - - + +
333B PHE* 3.8 18.4 - - + -
337B LEU* 4.1 19.1 - - + -
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Residues in contact with THR 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B LEU* 5.2 3.7 - - + +
119B THR* 2.7 31.8 + - - +
120B ILE* 3.6 5.8 - - - -
122B ALA* 1.3 77.9 - - - +
124B LEU* 1.3 67.9 + - + +
126B ALA* 3.5 6.4 + - - +
127B ALA* 3.3 20.3 + - - +
402B NAD 6.1 3.4 - - - +
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Residues in contact with LEU 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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30B LEU* 3.9 19.2 - - + +
56B TYR* 3.9 29.8 - - + -
86B LEU* 4.1 12.3 - - + -
98B ILE* 3.9 17.0 - - + -
100B ALA* 3.3 34.3 - - + -
120B ILE* 3.0 30.1 + - + +
121B VAL 4.2 1.3 - - - +
123B THR* 1.3 79.9 - - + +
125B THR* 1.3 60.0 + - - +
127B ALA* 3.2 8.9 + - - +
128B CYS* 3.0 30.0 + - - -
402B NAD 4.0 11.7 - - + +
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Residues in contact with THR 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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98B ILE* 3.9 21.5 - - + -
121B VAL* 2.6 32.5 + - + +
122B ALA* 3.5 6.8 + - - -
124B LEU* 1.3 72.4 - - - +
126B ALA* 1.3 62.7 + - - +
128B CYS* 3.2 8.6 + - - +
129B ALA* 2.9 26.5 + - - +
137B ILE* 4.5 3.1 - - + -
139B VAL* 5.0 0.4 - - + -
151B THR* 3.5 41.8 - - + +
154B VAL* 3.7 15.8 - - - +
155B PHE* 3.5 9.9 - - - -
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Residues in contact with ALA 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 ALA 3.1 22.1 + - - +
123B THR* 3.5 8.1 - - - +
124B LEU 3.3 0.2 - - - -
125B THR* 1.3 77.3 + - - +
127B ALA* 1.3 60.8 + - - +
129B ALA* 3.4 3.3 + - - +
130B GLN* 3.1 35.8 + - - +
154B VAL* 3.4 17.0 - - + +
158B HIS* 3.8 15.4 + - + +
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Residues in contact with ALA 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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86B LEU* 3.5 31.4 - - + -
87B PRO* 6.4 0.2 - - + -
90B LEU* 3.7 9.4 - - + -
123B THR 3.3 6.9 + - - +
124B LEU 3.2 10.6 + - - +
126B ALA* 1.3 78.4 - - - +
128B CYS* 1.3 57.1 + - - +
130B GLN* 3.3 4.9 + - - +
131B HIS* 2.9 47.5 + - + +
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Residues in contact with CYS 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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30B LEU* 4.0 9.6 - - - -
90B LEU* 4.1 10.5 - - - -
96B VAL* 3.7 33.7 - - - -
98B ILE* 4.5 4.0 - - - -
124B LEU 3.0 18.3 + - - -
125B THR* 3.2 14.1 + - - +
127B ALA* 1.3 74.3 - - - +
129B ALA* 1.3 62.0 + - - +
132B CYS* 2.8 43.2 + - - -
137B ILE* 4.1 10.8 - - + -
155B PHE* 4.1 13.9 - - + -
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Residues in contact with ALA 129 (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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125B THR 2.9 16.3 + - - +
126B ALA* 3.7 2.5 - - - +
128B CYS* 1.3 75.1 - - - +
130B GLN* 1.3 59.8 + - - +
133B PRO* 3.3 22.0 - - - +
154B VAL 4.5 0.4 - - - +
155B PHE* 3.8 22.3 - - + -
158B HIS* 3.7 35.1 - - + +
160B VAL* 3.8 19.3 - - + +
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Residues in contact with GLN 130 (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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126B ALA* 3.1 24.3 + - - +
127B ALA* 3.7 6.9 - - - +
129B ALA* 1.3 80.0 - - - +
131B HIS* 1.3 80.9 + - + +
133B PRO* 4.3 5.0 - - - +
158B HIS* 3.2 33.7 + - + -
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Residues in contact with HIS 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B PRO* 3.6 47.5 + - + +
90B LEU* 4.0 21.6 - - + +
91B LYS* 4.2 23.0 - - - +
92B GLY 4.6 2.4 + - - -
127B ALA* 2.9 35.4 + - + +
130B GLN* 1.3 99.0 + - + +
132B CYS* 1.3 62.3 + - - +
133B PRO* 3.6 4.7 - - - +
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Residues in contact with CYS 132 (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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90B LEU* 3.3 38.4 - - - +
92B GLY 4.9 1.1 - - - +
93B CYS* 4.2 10.5 - - + +
96B VAL* 3.7 29.2 - - - -
128B CYS* 2.8 26.7 + - - +
131B HIS* 1.3 73.0 - - - +
133B PRO* 1.3 65.8 - - - +
134B GLU 3.1 3.1 - - - -
135B ALA* 3.0 22.4 + - + +
137B ILE* 4.7 3.1 - - - +
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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