Contacts of the helix formed by residues 123 - 141 (chain B) in PDB entry 4LOU
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 ARG 123 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B TYR 4.2 1.6 + - - -
101B ALA* 4.6 0.4 - - - +
102B PRO* 4.0 15.2 - - - +
103B GLU* 3.3 43.5 + - - +
120B ARG* 6.1 1.0 - - - +
121B PRO* 3.8 24.8 + - + +
122B VAL* 1.3 71.8 - - - +
124B TRP* 1.3 62.9 + - - +
125B TRP* 3.3 31.9 - - + -
126B ARG* 3.0 40.5 + - + +
127B VAL* 3.0 23.3 + - - +
157B ASN* 4.0 4.1 + - - -
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Residues in contact with TRP 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B VAL 3.2 4.5 + - - +
123B ARG* 1.3 73.6 - - - +
125B TRP* 1.3 111.9 + + + +
126B ARG 3.1 0.9 + - - -
128B LEU* 3.3 32.7 + - + +
129B PRO* 4.0 0.3 - - - +
157B ASN* 3.6 37.2 - - + +
160B ARG* 4.0 10.3 - - + -
161B MET* 3.5 56.2 - - + +
164B ASP* 3.0 31.9 + - + -
165B ILE* 4.9 12.1 - - + -
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Residues in contact with TRP 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B VAL 4.0 7.4 - - - -
123B ARG* 3.7 32.3 - - + +
124B TRP* 1.3 131.7 - + + +
126B ARG* 1.3 87.1 + - + +
129B PRO* 3.7 15.8 - - - +
164B ASP* 5.2 2.9 - - - -
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Residues in contact with ARG 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B LYS 4.9 2.6 + - - -
100B TYR* 3.1 44.6 + - + +
101B ALA* 4.0 6.5 - - + -
123B ARG* 3.0 45.1 + - + +
125B TRP* 1.3 103.6 - - + +
127B VAL* 1.3 59.6 + - + +
128B LEU 3.8 0.2 - - - -
129B PRO* 3.6 4.4 - - - +
130B VAL* 3.1 32.7 + - - +
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Residues in contact with VAL 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ALA* 3.9 13.7 - - + -
103B GLU* 3.5 28.3 - - + +
104B ALA* 3.6 20.2 - - + -
123B ARG* 3.0 15.9 + - - +
124B TRP 3.3 0.2 + - - -
126B ARG* 1.3 79.7 - - + +
128B LEU* 1.3 60.5 + - + +
129B PRO 3.4 0.4 - - - -
130B VAL* 4.4 0.4 - - - -
131B LYS* 2.7 41.2 + - + +
153B GLN* 3.9 25.6 - - + +
154B ILE* 5.8 0.4 - - - +
157B ASN* 3.2 24.5 - - - +
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Residues in contact with LEU 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B TRP* 3.3 25.0 + - + +
127B VAL* 1.3 76.9 - - - +
129B PRO* 1.4 71.0 - - + +
132B PHE* 3.0 25.7 + - - +
154B ILE* 3.5 45.5 - - + +
157B ASN* 3.5 15.0 - - + -
158B ILE* 4.1 15.5 - - + +
161B MET* 3.9 28.3 - - - -
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Residues in contact with PRO 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B LEU* 5.4 2.9 - - + +
124B TRP 4.0 0.7 - - - +
125B TRP* 3.7 20.6 - - - +
126B ARG* 3.6 12.6 - - - +
128B LEU* 1.4 93.8 - - + +
130B VAL* 1.3 60.9 + - + +
132B PHE* 4.4 0.4 - - + -
133B PHE* 2.9 55.3 + - + +
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Residues in contact with VAL 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B LEU* 3.1 42.0 - - + +
97B VAL* 3.6 24.9 - - + +
100B TYR* 3.6 21.3 - - + -
101B ALA* 3.8 8.3 - - + -
104B ALA* 3.9 12.3 - - + -
126B ARG 3.1 21.1 + - - +
127B VAL* 3.2 2.9 + - - +
129B PRO* 1.3 79.7 - - + +
131B LYS* 1.3 56.1 + - - +
134B GLY* 2.6 35.6 + - - +
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Residues in contact with LYS 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B PHE* 4.1 3.8 - - - -
97B VAL* 6.0 0.2 - - - -
104B ALA* 2.6 33.7 + - + +
105B GLY 3.8 0.6 + - - -
106B GLY 2.6 27.1 + - - -
107B SER 3.6 5.7 + - - -
127B VAL* 2.7 26.9 + - + +
130B VAL* 1.3 72.2 - - - +
132B PHE* 1.3 58.5 + - - +
135B GLY* 2.7 31.6 + - - +
150B PRO* 3.7 32.7 - - + +
153B GLN* 3.0 29.9 + - + +
154B ILE* 3.8 23.1 - - + -
353B PRO* 4.2 12.3 - - + +
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Residues in contact with PHE 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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49B ALA* 3.7 28.9 - - + -
52B ALA* 3.7 25.6 - - + -
53B PHE* 3.5 18.5 - + + -
128B LEU 3.0 21.9 + - - +
129B PRO* 3.8 2.5 - - + +
131B LYS* 1.3 76.8 - - - +
133B PHE* 1.3 81.6 + + + +
136B LEU* 2.9 56.3 + - + +
154B ILE* 3.8 23.8 - - + +
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Residues in contact with PHE 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B PHE* 3.6 28.5 - + + -
96B LEU* 5.3 4.7 - - + -
129B PRO* 2.9 45.4 + - + +
132B PHE* 1.3 91.8 - + + +
134B GLY* 1.3 66.4 + - - +
136B LEU* 3.3 27.2 + - + +
137B GLY 3.4 8.3 + - - -
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Residues in contact with GLY 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B PHE* 4.6 1.5 - - - -
93B GLY* 3.5 28.4 - - - -
96B LEU* 4.4 10.6 - - - +
97B VAL* 5.3 0.4 - - - -
130B VAL* 2.6 24.5 + - - +
133B PHE* 1.3 71.9 - - - +
135B GLY* 1.3 62.4 + - - +
137B GLY 3.3 8.0 + - - -
138B THR* 3.3 14.4 + - - -
353B PRO* 3.7 9.5 - - - +
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Residues in contact with GLY 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B PHE* 3.8 16.4 - - - -
131B LYS* 2.7 22.8 + - - -
132B PHE 3.8 0.2 - - - -
134B GLY* 1.3 72.2 - - - +
136B LEU* 1.3 60.5 + - - +
137B GLY 2.9 5.6 + - - -
138B THR* 3.1 7.8 + - - -
139B LEU* 3.0 28.3 + - - +
150B PRO* 5.6 2.7 - - - -
353B PRO* 4.2 11.9 - - - +
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Residues in contact with LEU 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B PHE* 3.5 20.2 - - + +
56B GLY* 3.7 12.6 - - - -
57B VAL* 3.5 33.9 - - + +
60B LEU* 3.2 28.1 - - + +
132B PHE* 2.9 47.8 + - + +
133B PHE* 3.3 24.2 + - + +
135B GLY* 1.3 74.5 - - - +
137B GLY* 1.3 55.5 + - - +
140B GLY* 3.0 21.0 + - - +
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Residues in contact with GLY 137 (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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89B LEU* 3.3 41.8 - - - +
90B ALA* 4.0 0.3 + - - +
92B PHE* 5.0 4.5 - - - -
93B GLY 5.0 0.2 - - - -
133B PHE 3.4 6.5 + - - -
134B GLY 3.3 6.7 + - - -
135B GLY 2.9 2.2 + - - -
136B LEU* 1.3 78.1 - - - +
138B THR* 1.3 60.0 + - - +
141B GLY* 2.9 27.9 + - - -
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Residues in contact with THR 138 (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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89B LEU 4.1 0.6 + - - -
90B ALA* 4.3 17.3 - - - +
93B GLY* 4.6 1.6 - - - -
94B TYR* 4.4 4.0 - - + -
134B GLY 3.3 9.4 + - - +
135B GLY* 3.1 9.4 + - - -
137B GLY* 1.3 74.5 - - - +
139B LEU* 1.3 64.6 + - - +
141B GLY 4.0 0.2 - - - -
142B GLY 3.4 2.1 + - - -
143B MET* 3.1 57.0 + - - +
145B LEU* 4.5 3.8 - - - -
352B ALA* 3.9 17.0 - - + -
353B PRO* 3.0 35.2 + - + +
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Residues in contact with LEU 139 (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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53B PHE* 4.0 11.7 - - + -
57B VAL* 3.8 16.2 - - + +
61B GLN* 3.8 10.9 + - - -
135B GLY* 3.0 15.9 + - - +
138B THR* 1.3 85.1 + - - +
140B GLY* 1.3 60.3 + - - +
142B GLY* 2.9 22.0 + - - -
143B MET 4.7 5.4 - - - +
145B LEU* 3.8 35.4 - - + +
146B GLY* 3.6 5.4 - - - +
147B ARG* 3.5 54.1 - - + +
150B PRO* 5.2 1.3 - - + -
353B PRO 4.1 7.4 - - - +
354B GLY* 4.4 3.4 - - - -
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Residues in contact with GLY 140 (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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57B VAL* 3.7 23.5 - - - +
60B LEU* 3.9 12.3 - - - +
61B GLN* 3.5 14.9 + - - +
64B ARG* 3.1 19.9 + - - -
89B LEU* 4.3 2.5 - - - -
136B LEU 3.0 22.6 + - - -
139B LEU* 1.3 76.5 - - - +
141B GLY* 1.3 55.9 + - - +
142B GLY 3.1 1.2 + - - -
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Residues in contact with GLY 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ARG* 2.6 30.4 + - - -
86B SER* 3.0 21.8 + - - -
89B LEU* 4.1 17.2 - - - +
90B ALA* 6.3 0.2 - - - -
137B GLY 2.9 19.9 + - - -
138B THR 4.0 1.6 - - - -
140B GLY* 1.3 76.7 - - - +
142B GLY* 1.3 57.1 + - - +
143B MET* 3.7 3.1 - - - -
299B GLY 4.5 0.2 - - - +
303B GLY* 4.0 1.6 + - - -
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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