Contacts of the helix formed by residues 115 - 129 (chain B) in PDB entry 3L73
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 HIS 115 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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359A ASN* 4.4 15.8 + - - -
92B VAL* 3.6 55.9 + - + +
111B CYS* 3.7 8.5 - - + -
112B LEU* 2.9 34.0 + - + +
114B ASP* 1.3 93.7 + - + +
116B VAL* 1.3 69.6 + - - +
117B ASP* 3.4 3.4 - - - -
118B THR* 3.1 17.7 + - - +
119B VAL* 3.1 12.3 + - - +
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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
----------------------------------------------------------
45B SER* 3.1 36.6 - - - +
47B ILE* 3.2 31.7 - - + +
111B CYS* 3.6 12.0 - - - -
113B ARG 3.3 17.7 + - - +
114B ASP 3.6 1.6 - - - -
115B HIS* 1.3 77.0 - - - +
117B ASP* 1.3 70.2 + - - +
118B THR 2.9 1.0 + - - -
119B VAL* 3.0 2.1 + - - +
120B MET* 2.9 26.7 + - + +
211B VAL* 4.1 13.2 - - + -
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Residues in contact with ASP 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ARG 5.2 0.5 - - - +
114B ASP 3.9 13.1 - - - +
116B VAL* 1.3 86.3 + - - +
118B THR* 1.3 73.0 + - - +
120B MET* 3.5 16.1 - - - +
121B GLU* 3.7 6.8 + - - +
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Residues in contact with THR 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B GLY 5.0 5.6 - - - +
92B VAL* 4.8 15.1 - - + +
114B ASP 5.1 0.7 + - - -
115B HIS* 3.1 20.3 + - - +
116B VAL 2.9 2.2 + - - -
117B ASP* 1.3 84.6 + - - +
119B VAL* 1.3 66.4 + - + +
120B MET 3.1 2.0 + - - -
121B GLU* 3.3 17.5 + - - +
122B TYR* 3.4 27.6 - - + +
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Residues in contact with VAL 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ILE* 6.5 0.2 - - + -
89B ILE* 4.6 12.3 - - + +
92B VAL* 3.9 21.3 - - + -
94B GLY* 4.9 2.5 - - - -
95B SER 4.4 5.2 - - - +
109B VAL* 3.2 38.4 - - + +
110B GLU 4.4 7.4 - - - +
111B CYS* 3.6 26.0 - - + -
115B HIS 3.4 13.0 - - - +
116B VAL 3.0 5.3 + - - +
118B THR* 1.3 75.5 - - + +
120B MET* 1.3 61.7 + - - +
121B GLU 3.4 0.2 + - - -
122B TYR* 3.6 13.4 + - - +
123B LEU* 3.3 16.8 + - - +
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Residues in contact with MET 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ILE* 3.0 51.8 - - + +
109B VAL* 5.5 0.9 - - - -
116B VAL* 2.9 19.2 + - + +
117B ASP* 3.5 13.0 - - - +
118B THR 3.1 0.2 - - - -
119B VAL* 1.3 76.2 - - - +
121B GLU* 1.3 66.4 + - - +
123B LEU* 3.0 20.3 + - - +
124B LEU* 2.8 28.3 + - + +
206B LEU* 5.0 4.3 - - + -
216B LEU* 4.0 14.8 - - + -
219B VAL* 3.8 40.4 - - + -
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Residues in contact with GLU 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B GLY 4.6 1.6 - - - +
84B ARG* 2.8 31.6 + - - +
117B ASP 3.7 6.2 + - - +
118B THR* 3.3 15.2 + - - +
120B MET* 1.3 78.2 - - - +
122B TYR* 1.3 78.0 + - + +
124B LEU* 3.3 10.4 + - - +
125B ASN* 2.8 49.1 + - - +
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Residues in contact with TYR 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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80B ALA* 3.7 19.7 - - + -
84B ARG* 3.6 49.6 + - - +
85B ILE* 3.6 24.9 - - + -
88B GLY* 3.7 26.8 - - - -
89B ILE* 3.7 32.3 - - + -
96B LEU* 5.6 0.4 - - - -
118B THR* 3.4 31.6 - - + +
119B VAL* 4.0 7.2 - - - +
120B MET 3.3 0.4 - - - -
121B GLU* 1.3 84.1 + - + +
123B LEU* 1.3 58.3 + - - +
125B ASN* 4.0 5.2 - - - -
126B VAL* 2.7 42.2 + - + +
107S TRP* 4.7 2.3 - - - -
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Residues in contact with LEU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ILE* 4.0 31.4 - - + +
49B VAL* 4.0 19.3 - - + -
96B LEU* 5.3 4.5 - - + +
107B TYR* 3.4 42.2 - - + +
109B VAL* 4.1 29.9 - - + +
119B VAL 3.3 11.0 + - - +
120B MET* 3.0 20.7 + - - +
122B TYR* 1.3 80.1 - - - +
124B LEU* 1.3 64.0 + - - +
126B VAL* 3.7 3.8 - - + +
127B THR* 3.1 24.3 + - + +
206B LEU* 5.2 0.9 - - + -
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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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49B VAL* 6.2 0.7 - - - -
120B MET* 2.8 19.5 + - + +
121B GLU* 3.5 13.2 - - - +
123B LEU* 1.3 75.0 - - - +
125B ASN* 1.3 73.3 + - - +
127B THR* 3.2 5.3 + - - -
128B THR* 2.7 45.5 + - - +
129B ALA* 5.6 1.8 - - + -
219B VAL* 5.4 7.4 - - + -
223B PHE* 3.2 54.3 - - + +
224B LEU* 4.4 17.5 - - + -
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Residues in contact with ASN 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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77B THR* 3.4 21.2 + - + +
79B GLY* 2.8 41.1 + - - -
80B ALA* 3.9 4.1 - - + +
85B ILE* 6.0 0.2 - - + -
121B GLU* 2.8 44.8 + - - +
122B TYR* 3.5 7.6 - - - +
124B LEU* 1.3 85.5 - - - +
126B VAL* 1.3 64.7 + - + +
128B THR* 4.3 1.1 - - - -
129B ALA* 2.9 36.6 + - - +
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Residues in contact with VAL 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B SER* 3.5 35.9 - - - +
77B THR* 3.8 7.8 - - + +
85B ILE* 4.5 15.5 - - + -
96B LEU* 4.5 18.2 - - + -
107B TYR* 3.7 28.3 - - + -
122B TYR* 2.7 35.5 + - + +
123B LEU* 3.7 5.2 - - + +
125B ASN* 1.3 75.6 - - - +
127B THR* 1.3 62.7 + - + +
130B PRO* 3.5 21.0 - - - +
199B PHE* 5.9 0.3 - - - -
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Residues in contact with THR 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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49B VAL* 4.3 23.0 - - + +
51B ILE* 5.0 1.3 - - + -
107B TYR* 3.3 48.2 - - + -
123B LEU* 3.1 22.4 + - + +
124B LEU* 3.2 8.8 + - - -
126B VAL* 1.3 75.1 - - - +
128B THR* 1.3 66.2 + - - +
130B PRO* 4.4 3.6 - - - +
195B VAL* 4.7 0.5 - - - +
199B PHE* 3.4 35.3 - - - +
204B MET* 5.2 3.7 - - - +
224B LEU* 5.1 1.6 - - - +
226B ILE* 4.5 2.3 - - - +
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Residues in contact with THR 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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78B LYS* 5.7 0.7 + - - -
124B LEU* 2.7 35.6 + - - +
127B THR* 1.3 84.1 - - - +
129B ALA* 1.3 63.3 + - - +
130B PRO* 3.4 8.8 - - - +
204B MET* 5.0 9.4 - - + -
224B LEU* 3.6 33.4 - - + -
225B ASN* 4.9 10.2 + - - +
226B ILE* 2.9 40.8 - - + +
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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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77B THR* 3.5 1.6 - - - -
78B LYS* 3.0 48.1 + - + +
124B LEU* 5.6 1.8 - - + -
125B ASN* 2.9 28.3 + - - +
128B THR* 1.3 85.3 + - - +
130B PRO* 1.3 66.6 - - - +
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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
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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