Contacts of the helix formed by residues 106 - 124 (chain B) in PDB entry 5LF4
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 106 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B TYR* 3.5 21.3 - - + +
103B GLU* 4.8 1.1 - - - +
104B PRO 3.4 8.3 - - - +
105B ILE* 1.3 87.4 - - + +
107B CYS* 1.3 65.9 - - - +
108B GLU* 3.3 3.1 - - + +
109B GLN* 3.0 40.9 + - + +
110B LEU* 3.3 8.8 + - - +
140B ASP* 3.5 20.0 - - + +
142B HIS* 3.7 32.3 - - + +
143B TYR* 6.3 0.9 - - + -
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Residues in contact with CYS 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B MET* 3.7 34.2 - - + +
105B ILE 3.5 1.3 + - - -
106B PRO* 1.3 70.2 - - - +
108B GLU* 1.3 63.1 + - - +
110B LEU* 3.0 14.4 + - - +
111B VAL* 3.1 18.2 + - - +
137B ILE 6.1 0.2 - - - -
138B GLY* 3.8 24.7 - - - -
139B TRP 3.8 13.0 - - - -
140B ASP* 3.0 16.7 + - - -
146B GLN* 3.6 25.8 - - + +
148B TYR* 4.0 10.8 - - + -
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Residues in contact with GLU 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B PRO* 3.3 2.3 - - + +
107B CYS* 1.3 78.8 - - - +
109B GLN* 1.3 60.3 + - + +
111B VAL* 3.5 5.1 + - - +
112B THR* 2.8 36.0 + - - +
140B ASP* 4.7 0.4 + - - -
143B TYR* 4.7 6.0 - - + -
146B GLN* 4.3 2.3 + - - +
148B TYR* 3.6 23.9 - - + +
156B TYR* 2.7 41.8 + - + +
57C ARG* 2.7 37.5 + - - -
58C THR* 4.0 11.3 - - - +
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Residues in contact with GLN 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B TYR* 3.4 27.6 + - - -
105B ILE* 3.9 11.9 - - + +
106B PRO* 3.0 40.1 + - + +
108B GLU* 1.3 77.6 - - + +
110B LEU* 1.3 57.8 - - - +
112B THR* 3.9 5.9 - - - -
113B ALA* 3.0 28.6 + - - +
142B HIS* 5.5 0.9 - - - -
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Residues in contact with LEU 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B LEU* 4.1 25.4 - - + -
69B ASN* 5.1 0.4 - - - +
72B MET* 3.6 29.2 - - + -
90B LEU* 3.4 40.1 - - + +
93B ILE* 3.6 21.5 - - + -
94B ALA* 4.0 8.3 - - + +
105B ILE* 3.7 23.7 - - + +
106B PRO 3.3 4.2 + - - +
107B CYS 3.0 9.9 + - - +
109B GLN* 1.3 74.6 - - - +
111B VAL* 1.3 68.2 + - + +
113B ALA* 3.3 3.3 + - - +
114B LEU* 3.1 20.6 + - - +
136B TYR* 5.5 0.4 - - + -
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Residues in contact with VAL 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B MET* 4.8 1.8 - - + -
107B CYS 3.1 13.8 + - - +
108B GLU* 3.7 7.4 - - - +
110B LEU* 1.3 76.9 - - - +
112B THR* 1.3 56.2 - - - +
114B LEU* 3.2 4.4 + - - +
115B CYS* 2.9 31.0 + - - -
136B TYR* 3.6 55.4 - - + -
148B TYR* 3.9 17.5 - - + -
156B TYR* 3.5 39.9 - - + -
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Residues in contact with THR 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B GLU* 2.8 23.9 + - - +
109B GLN* 3.9 6.5 - - - -
110B LEU 3.3 0.2 - - - -
111B VAL* 1.3 73.4 - - - +
113B ALA* 1.3 66.0 + - - +
115B CYS* 3.3 6.4 + - - +
116B ASP* 3.0 31.5 + - - +
156B TYR* 3.6 22.5 + - - +
81C ARG* 3.7 29.2 - - + +
85C ASN* 5.1 5.6 - - - +
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Residues in contact with ALA 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ILE* 3.7 31.6 - - + -
105B ILE* 5.5 0.4 - - + -
109B GLN 3.0 17.9 + - - +
110B LEU 3.7 4.9 - - - +
111B VAL 3.3 0.2 - - - -
112B THR* 1.3 77.0 - - - +
114B LEU* 1.3 63.6 + - - +
116B ASP* 3.4 13.8 + - - +
117B ILE* 3.5 14.6 + - - +
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Residues in contact with LEU 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B LEU* 3.9 45.5 - - + +
89B GLU* 4.4 17.7 - - + -
90B LEU* 3.7 34.8 - - + +
93B ILE* 4.2 5.7 - - + +
110B LEU 3.1 6.7 + - - -
111B VAL 3.7 6.5 - - - +
113B ALA* 1.3 74.4 - - - +
115B CYS* 1.3 64.7 + - - +
117B ILE* 2.9 22.7 + - + +
118B LYS* 3.0 21.8 + - + +
134B LEU* 4.4 8.7 - - + -
136B TYR* 3.3 22.7 - - - +
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Residues in contact with CYS 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 VAL* 2.9 20.0 + - - +
112B THR* 3.7 5.8 - - - +
114B LEU* 1.3 76.8 - - - +
116B ASP* 1.3 56.6 + - - +
118B LYS* 3.4 10.8 + - - +
119B GLN* 2.8 24.8 + - - +
136B TYR* 4.8 1.1 - - - -
150B SER* 3.5 32.5 - - - -
154B GLY* 3.3 23.3 - - - +
155B ASN 4.0 2.2 - - - -
156B TYR* 3.7 19.5 - - + -
81C ARG* 3.3 17.2 + - - +
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Residues in contact with ASP 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B THR* 3.0 23.5 + - - +
113B ALA* 3.7 10.9 - - - +
114B LEU 3.1 0.4 - - - -
115B CYS* 1.3 75.4 - - - +
117B ILE* 1.3 59.4 + - + +
119B GLN* 3.7 6.2 - - - +
120B ALA* 3.1 27.5 + - - +
81C ARG* 2.6 35.4 + - - +
82C ILE* 3.6 22.8 - - + +
85C ASN* 4.7 9.2 + - - +
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Residues in contact with ILE 117 (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 4.5 - - + -
89B GLU* 3.6 37.0 - - + +
93B ILE* 4.3 8.5 - - + -
113B ALA 3.5 13.7 + - - +
114B LEU* 2.9 15.8 + - + +
116B ASP* 1.3 73.7 - - + +
118B LYS* 1.3 68.5 + - - +
120B ALA* 3.2 14.7 + - - +
121B TYR* 3.3 32.3 + - + -
130B PHE* 4.9 7.6 - - + -
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Residues in contact with LYS 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B LEU* 4.1 26.5 - - + -
114B LEU* 3.0 19.0 + - + +
115B CYS* 3.7 23.6 - - - +
117B ILE* 1.3 75.9 - - - +
119B GLN* 1.3 63.4 + - - +
121B TYR* 3.1 21.5 + - - +
122B THR* 3.5 11.6 + - - +
129B PRO* 5.7 0.3 - - - +
130B PHE* 4.7 15.7 - - + -
132B VAL 4.0 4.2 + - - +
134B LEU* 3.8 14.3 - - - +
150B SER* 2.9 28.9 + - - -
151B ASP* 3.2 29.6 + - - +
152B PRO* 4.3 12.2 - - + +
154B GLY* 3.9 10.8 - - - +
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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 CYS 2.8 20.3 + - - +
116B ASP* 3.7 6.6 - - - +
117B ILE 3.3 0.2 - - - -
118B LYS* 1.3 71.0 - - - +
120B ALA* 1.3 71.5 + - - +
122B THR* 2.6 29.5 + - - +
123B GLN* 2.9 33.2 + - - +
124B PHE* 5.4 1.0 - - - -
153B SER 4.2 7.2 - - - +
154B GLY* 4.1 1.0 - - - -
78C ALA* 3.7 31.9 - - + +
79C ASP* 2.9 27.5 + - - +
81C ARG* 4.2 8.7 - - - +
82C ILE* 3.4 22.5 - - + +
125C ARG* 4.0 0.8 - - - +
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Residues in contact with ALA 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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116B ASP 3.1 12.1 + - - +
117B ILE* 3.2 12.3 + - - +
119B GLN* 1.3 85.1 + - - +
121B TYR* 1.3 59.8 + - + +
123B GLN* 3.0 2.9 + - - +
124B PHE* 2.9 66.0 + - + +
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Residues in contact with TYR 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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122A GLN* 3.6 22.4 - - + +
9B THR 5.2 0.5 - - - +
10B THR* 3.3 18.3 - - - +
117B ILE* 3.3 28.8 + - + -
118B LYS* 3.1 14.1 + - - +
120B ALA* 1.3 80.4 - - + +
122B THR* 1.3 58.3 + - - +
123B GLN 3.4 0.2 - - - -
124B PHE 4.1 5.7 - - - +
127B LYS* 3.8 35.8 + - + +
128B ARG 3.6 17.9 - - - -
129B PRO* 4.5 15.6 - - + +
130B PHE* 3.6 33.2 - + + +
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Residues in contact with THR 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B THR 5.1 2.2 - - - +
10B THR* 3.7 16.7 - - - +
18B LEU* 4.3 10.5 - - + +
21B VAL* 3.4 32.5 - - + -
118B LYS 3.6 15.0 - - - +
119B GLN* 2.6 21.0 + - - +
121B TYR* 1.3 77.3 - - - +
123B GLN* 1.3 57.6 + - - +
129B PRO* 5.0 4.9 - - + -
152B PRO 3.8 11.7 - - - +
153B SER* 4.2 9.9 + - - +
79C ASP* 4.6 0.3 + - - -
125C ARG* 2.9 34.5 + - - -
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Residues in contact with GLN 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B THR* 3.9 7.0 - - - -
119B GLN* 2.9 30.3 + - - +
120B ALA 3.0 4.8 + - - +
122B THR* 1.3 82.8 + - - +
124B PHE* 1.3 67.9 + - + +
82C ILE* 5.1 1.2 - - - +
118C TYR* 3.3 26.7 - - + -
123C GLY 3.9 0.2 - - - +
124C ARG* 3.4 0.5 - - - -
125C ARG* 3.0 67.1 + - + +
126C PRO 3.7 7.7 + - - -
127C PHE* 3.3 32.6 - - - +
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Residues in contact with PHE 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B THR* 3.7 9.1 - - - +
119B GLN* 5.4 1.3 - - - -
120B ALA* 2.9 49.4 + - + +
121B TYR* 4.1 6.1 - - - -
122B THR 3.9 0.2 - - - -
123B GLN* 1.3 90.3 - - + +
125B GLY* 1.3 67.5 + - - +
126B GLY 3.5 3.7 + - - -
127B LYS* 4.9 1.4 + - - +
118C TYR* 5.2 10.3 - + - -
123C GLY 3.2 17.3 - - - +
124C ARG* 3.9 19.3 - - + -
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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
------------------------------------------------------------
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