Contacts of the helix formed by residues 93 - 111 (chain B) in PDB entry 3LB2
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 THR 93 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B TYR* 6.0 1.1 - - - +
91B SER 4.8 4.3 - - - +
92B LEU* 1.3 79.2 - - - +
94B THR* 1.3 66.7 + - - +
95B GLY* 3.3 13.0 + - - -
96B ASN* 2.9 29.9 + - - +
97B PHE* 3.6 7.1 - - - -
136B MET* 3.5 11.9 - - - -
137B LYS 3.8 19.7 - - - +
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Residues in contact with THR 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B THR* 1.3 75.0 - - - +
95B GLY* 1.3 58.6 + - - +
97B PHE* 3.1 10.1 + - - +
98B GLU* 2.9 26.9 + - - +
128B VAL* 3.8 38.9 - - + +
131B LEU* 4.0 17.3 - - + -
132B SER* 4.1 9.0 - - - +
136B MET* 3.6 25.9 - - + +
137B LYS 4.1 8.2 - - - +
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Residues in contact with GLY 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B THR* 3.1 9.6 + - - -
94B THR* 1.3 80.5 + - - +
96B ASN* 1.3 61.8 + - - +
98B GLU* 3.3 8.9 + - - +
99B LYS* 3.1 34.8 + - - +
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Residues in contact with ASN 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B PHE* 4.1 3.8 - - - -
31B GLU* 2.8 29.4 + - - -
34B TYR* 3.2 31.2 + - - -
92B LEU* 3.5 16.0 - - + -
93B THR* 2.9 37.8 + - - +
95B GLY* 1.3 75.5 - - - +
97B PHE* 1.3 63.6 + - + +
99B LYS* 3.5 5.6 + - - +
100B LEU* 3.1 17.2 + - - +
139B HEM 3.5 27.6 - - + +
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Residues in contact with PHE 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B LEU* 4.9 7.6 - - + -
89B HIS* 4.1 12.8 - + - -
92B LEU* 3.8 24.5 - - + -
93B THR 3.6 13.5 - - - -
94B THR 3.1 6.8 + - - +
96B ASN* 1.3 77.6 - - + +
98B GLU* 1.3 65.4 + - - +
100B LEU* 3.2 2.6 + - + +
101B PHE* 3.0 34.1 + + + -
127B LEU* 4.7 3.8 - - + -
128B VAL* 4.1 8.5 - - + -
131B LEU* 3.6 28.5 - - + -
136B MET* 3.6 29.8 - - + -
139B HEM 3.4 58.6 - + + -
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Residues in contact with GLU 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B THR 2.9 12.7 + - - +
95B GLY* 3.3 13.4 + - - +
97B PHE* 1.3 76.5 - - - +
99B LYS* 1.3 62.9 + - + +
101B PHE* 3.2 6.6 + - - +
102B VAL* 2.9 45.4 + - - +
125B LYS* 5.2 8.1 + - + -
128B VAL* 4.1 18.3 - - + +
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Residues in contact with LYS 99 (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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24B PHE* 3.8 6.7 - - + -
28B TYR* 3.3 59.6 - - + +
30B ASP* 4.7 9.9 + - - -
31B GLU* 4.3 22.2 + - - -
95B GLY* 3.1 23.0 + - - +
96B ASN* 3.8 5.4 - - - +
97B PHE 3.2 0.2 - - - -
98B GLU* 1.3 80.6 - - - +
100B LEU* 1.3 65.2 + - - +
102B VAL* 3.2 1.0 + - - +
103B ALA* 3.1 19.6 + - - +
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Residues in contact with LEU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ILE* 4.8 6.5 - - + +
21B PHE* 5.1 2.0 - - + -
24B PHE* 3.5 36.6 - - + -
60B PHE* 4.8 14.1 - - + -
63B MET* 4.0 16.2 - - + -
96B ASN 3.1 14.0 + - - +
97B PHE* 3.2 7.6 + - + +
99B LYS* 1.3 76.2 - - - +
101B PHE* 1.3 65.7 + - + +
103B ALA* 3.3 2.1 + - - +
104B LEU* 2.9 27.3 + - + +
139B HEM 3.9 39.5 - - + -
192B BML 4.0 23.8 - - + -
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Residues in contact with PHE 101 (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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63B MET* 4.0 16.8 - - + -
97B PHE* 3.0 33.7 + + + +
98B GLU* 4.0 5.2 - - - +
100B LEU* 1.3 84.2 - - + +
102B VAL* 1.3 64.7 + - - +
104B LEU* 3.8 26.7 - - + -
105B VAL* 3.0 30.5 + - + +
120B TRP* 4.1 13.0 - + - +
121B ASP* 5.8 0.9 - - - +
123B PHE* 3.8 35.4 - + - -
124B GLY* 3.7 27.6 - - - -
127B LEU* 3.8 24.0 - - + -
128B VAL* 5.6 1.3 - - + -
139B HEM 4.1 10.1 - - + -
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Residues in contact with VAL 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B LYS* 3.9 5.4 - - - -
28B TYR* 3.3 25.4 - - - +
98B GLU* 2.9 42.3 + - - +
99B LYS 3.2 3.1 + - - +
101B PHE* 1.3 74.5 - - - +
103B ALA* 1.3 63.3 + - - +
105B VAL* 3.9 4.0 - - - +
106B GLU* 3.0 43.7 + - + +
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Residues in contact with ALA 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ILE* 4.8 2.7 - - - +
23B ALA* 4.1 9.4 - - + +
24B PHE* 3.6 38.1 - - + +
27B LYS* 4.7 7.6 - - + -
28B TYR* 4.5 6.3 - - + -
99B LYS 3.1 12.0 + - - +
100B LEU 3.6 7.9 - - - +
102B VAL* 1.3 78.9 - - - +
104B LEU* 1.3 56.3 + - - +
106B GLU* 3.4 6.6 + - - +
107B TYR* 2.9 30.1 + - - +
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Residues in contact with LEU 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ILE* 5.5 1.3 - - + -
20B ILE* 3.3 47.5 - - + +
60B PHE* 4.5 2.5 - - + -
63B MET* 3.8 35.0 - - + -
64B MET* 5.9 0.4 - - + -
100B LEU* 2.9 18.6 + - + +
101B PHE* 3.7 26.7 - - + +
102B VAL 3.3 0.2 - - - -
103B ALA* 1.3 76.1 - - - +
105B VAL* 1.3 58.3 + - - +
107B TYR* 3.3 2.7 + - - +
108B MET* 3.0 49.7 + - + +
120B TRP* 4.8 10.3 - - + -
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Residues in contact with VAL 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B PHE* 3.0 22.7 + - + +
102B VAL* 3.9 4.5 - - - +
104B LEU* 1.3 72.8 - - + +
106B GLU* 1.3 66.6 + - + +
108B MET* 3.2 8.2 + - - +
109B ARG* 3.0 57.3 + - - +
117B SER* 4.0 16.8 - - - +
120B TRP* 4.0 10.3 - - + +
121B ASP* 3.6 39.7 - - + +
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Residues in contact with GLU 106 (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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27B LYS* 3.2 44.8 + - - +
102B VAL* 3.0 28.5 + - + +
103B ALA* 3.6 5.4 - - - +
105B VAL* 1.3 77.2 - - + +
107B TYR* 1.3 64.5 + - - +
109B ARG* 3.3 13.8 + - - +
110B ALA* 3.1 24.3 + - - +
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Residues in contact with TYR 107 (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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16B TYR* 3.3 35.7 - + - -
19B ASP* 3.9 39.3 + - + +
20B ILE* 3.6 29.4 - - + -
23B ALA* 4.6 12.1 - - + -
103B ALA 2.9 17.9 + - - +
104B LEU* 3.5 6.3 - - - +
105B VAL 3.3 0.2 - - - -
106B GLU* 1.3 77.0 - - - +
108B MET* 1.3 69.4 + - + +
110B ALA* 3.2 6.1 + - + +
111B SER* 3.0 29.5 + - - -
115B PHE* 4.5 10.5 - + - -
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Residues in contact with MET 108 (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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9B ILE* 3.8 15.5 - - + -
20B ILE* 5.2 0.9 - - + -
104B LEU* 3.0 38.4 + - + +
105B VAL* 3.2 8.3 + - - +
107B TYR* 1.3 81.5 - - + +
109B ARG* 1.3 61.9 + - - +
111B SER* 2.7 26.7 + - - +
113B GLN 4.1 5.0 - - - +
115B PHE* 3.8 41.7 + - + +
117B SER* 4.0 11.9 - - - -
120B TRP* 3.4 57.4 - - + +
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Residues in contact with ARG 109 (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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105B VAL* 3.0 42.8 + - - +
106B GLU* 3.7 12.2 - - - +
107B TYR 3.3 0.2 - - - -
108B MET* 1.3 76.5 - - - +
110B ALA* 1.3 60.8 + - - +
111B SER 3.7 3.8 + - - +
117B SER* 3.4 23.2 + - - +
118B GLN* 5.7 6.9 - - - +
121B ASP* 3.9 14.6 + - - +
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Residues in contact with ALA 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B GLU 3.1 15.8 + - - +
107B TYR* 3.2 6.3 + - + +
109B ARG* 1.3 76.0 - - - +
111B SER* 1.3 63.6 + - - +
112B GLY 3.9 0.5 + - - -
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Residues in contact with SER 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B TYR* 6.0 0.7 - - - -
107B TYR* 3.0 26.6 + - - -
108B MET* 2.7 20.9 + - - +
109B ARG 4.2 3.6 - - - +
110B ALA* 1.3 81.5 - - - +
112B GLY* 1.3 60.8 + - - +
113B GLN* 3.1 22.1 + - - +
115B PHE* 3.2 19.5 - - - -
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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
------------------------------------------------------------
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