Contacts of the strand formed by residues 35 - 47 (chain B) in PDB entry 4LML
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 35 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B SER 3.6 0.9 - - - +
29B LEU* 4.8 1.3 - - - +
30B ASP* 2.7 26.9 + - - +
33B ALA* 3.3 20.8 - - + +
34B GLU* 1.3 85.7 - - - +
36B PHE* 1.3 62.8 + - - +
81B GLU* 3.6 16.2 - - - +
108B ARG* 2.5 37.6 + - - +
109B VAL 3.2 11.2 - - - +
110B LEU* 3.6 24.7 - - + -
111B SER 4.7 0.7 - - - +
113B LEU* 5.2 0.2 - - - +
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Residues in contact with PHE 36 (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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26B CYS* 4.7 13.0 - - - -
27B TYR 4.6 1.1 - - - +
28B SER 3.4 6.3 - - - -
29B LEU* 3.7 25.6 - - + +
35B THR* 1.3 76.6 - - - +
37B LYS* 1.3 75.0 + - - +
38B VAL* 4.3 8.7 - - + -
108B ARG* 3.2 7.9 - - - +
109B VAL* 2.8 70.3 + - + +
111B SER* 4.1 8.3 - - - -
125B LEU* 3.6 51.4 - - + -
126B HIS 4.5 0.2 - - - -
127B ILE* 3.9 20.0 - - + -
156B LEU* 5.2 3.6 - - + -
187B LEU* 5.1 4.9 - - + -
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Residues in contact with LYS 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B CYS* 3.7 7.3 - - - -
27B TYR* 3.1 68.7 + - + +
28B SER* 3.8 21.8 + - - +
36B PHE* 1.3 84.6 - - - +
38B VAL* 1.3 62.8 + - - +
107B ALA 3.7 4.5 - - - +
108B ARG* 3.9 36.8 - - + +
81E GLU* 4.6 8.1 + - - -
82E ASN* 6.4 0.4 - - - +
108E ARG* 6.2 0.2 - - - +
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Residues in contact with VAL 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LEU* 3.6 31.4 - - + -
25B GLU 3.9 2.2 - - - +
26B CYS* 4.2 11.4 - - - -
27B TYR* 5.0 4.5 + - - -
36B PHE* 4.3 11.8 + - + -
37B LYS* 1.3 74.8 - - - +
39B ASN* 1.3 63.9 + - - +
40B ALA* 4.3 9.0 - - + -
105B PHE* 4.0 22.8 - - + +
106B SER* 3.4 4.2 - - - -
107B ALA* 2.9 43.2 + - + +
109B VAL* 3.8 20.0 - - + -
127B ILE* 4.3 9.0 - - + -
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Residues in contact with ASN 39 (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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23B LEU* 4.4 0.2 - - - -
24B ILE* 2.9 22.8 + - - +
25B GLU* 3.0 29.8 + - + +
27B TYR* 4.6 4.3 - - + -
38B VAL* 1.3 75.3 - - - +
40B ALA* 1.3 61.6 + - - +
104B ARG* 3.0 42.8 + - - +
105B PHE 2.9 20.2 - - - +
106B SER* 4.0 6.6 - - - -
78E VAL 4.7 0.4 + - - -
80E VAL 3.6 16.6 + - - -
81E GLU 4.1 16.8 + - - +
82E ASN 5.8 2.2 - - - -
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Residues in contact with ALA 40 (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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21B ILE* 3.9 9.2 - - + -
22B TYR 3.1 19.1 - - - +
23B LEU* 3.7 16.2 - - + -
24B ILE* 3.7 10.5 - - - -
38B VAL* 4.2 2.0 - - + -
39B ASN* 1.3 75.4 + - - +
41B PHE* 1.3 60.3 + - - +
104B ARG* 3.3 6.8 - - - +
105B PHE* 2.9 54.5 + - + +
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Residues in contact with PHE 41 (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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20B GLY 4.6 0.2 - - - -
21B ILE* 3.3 12.5 - - - +
22B TYR* 2.9 54.8 + + + -
24B ILE* 3.9 18.4 - - + -
40B ALA* 1.3 71.5 - - - +
42B LEU* 1.3 59.1 + - - +
43B SER 4.2 0.2 - - - -
89B VAL* 4.2 17.9 - - + -
102B LEU* 3.4 31.4 - - + -
103B GLU 3.3 15.0 - - - -
104B ARG* 4.2 9.9 - - + -
105B PHE* 3.9 2.1 - - - -
76E ARG* 3.4 29.8 - - - -
130E ILE* 5.7 1.8 - - + -
132E ARG* 5.0 2.5 - - - -
175E LEU* 3.6 25.6 - - + -
176E GLU* 4.1 12.1 - - - +
180E GLU* 4.0 8.7 - - - -
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Residues in contact with LEU 42 (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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20B GLY 3.6 11.2 - - - +
21B ILE* 3.9 19.1 - - + -
41B PHE* 1.3 73.5 - - - +
43B SER* 1.3 68.8 + - - +
44B LEU* 4.1 26.4 + - + -
75B ILE* 4.7 11.0 - - + -
77B PHE* 4.6 9.0 - - + -
84B ARG* 3.9 17.0 - - - +
101B TYR* 4.0 2.0 - - + +
102B LEU* 3.3 7.3 - - - +
103B GLU* 2.9 65.8 + - + +
105B PHE* 4.0 12.7 - - + -
129B LEU* 4.1 15.0 - - + -
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Residues in contact with SER 43 (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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18B ASN 3.1 2.0 - - - +
19B THR* 3.1 9.5 - - - -
20B GLY 2.8 42.0 + - - -
41B PHE 5.0 0.7 + - - -
42B LEU* 1.3 73.6 - - - +
44B LEU* 1.3 63.2 + - - +
101B TYR 3.8 4.5 - - - -
102B LEU* 4.1 1.7 - - - +
146B GLU* 3.8 16.7 - - - +
176E GLU* 3.2 33.8 + - - -
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Residues in contact with LEU 44 (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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17B VAL* 4.0 14.1 - - + -
18B ASN 3.4 1.6 - - - -
19B THR* 4.0 24.7 - - + -
42B LEU* 4.1 18.8 + - + -
43B SER* 1.3 81.6 - - - +
45B SER* 1.3 62.7 + - - +
46B TRP* 3.8 20.2 - - + -
72B ILE* 5.3 1.6 - - + -
73B PRO* 4.9 7.0 - - + +
75B ILE* 3.5 32.8 - - + -
100B GLN* 4.1 1.4 - - - +
101B TYR* 2.9 61.4 + - + +
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Residues in contact with SER 45 (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 THR 4.2 1.0 - - - +
17B VAL* 3.8 0.5 - - - -
18B ASN* 3.0 50.8 + - - +
44B LEU* 1.3 76.8 - - - +
46B TRP* 1.3 64.9 + - - +
98B THR* 5.6 3.4 - - - -
99B VAL 3.2 9.6 - - - -
100B GLN* 3.5 23.8 - - - -
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Residues in contact with TRP 46 (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 PRO* 5.2 0.2 - - + -
15B LEU* 4.6 7.9 - - + -
16B THR 4.0 16.2 - - - +
17B VAL* 4.4 11.0 - - + -
18B ASN* 6.1 0.2 - - - +
44B LEU* 3.8 14.8 - - + -
45B SER* 1.3 84.9 - - - +
47B LYS* 1.3 63.8 + - - +
48B ASP* 3.7 26.6 + - + +
70B ILE* 4.5 0.4 - - + -
71B TRP* 3.5 38.1 + + - -
72B ILE* 3.9 17.7 - - + -
73B PRO* 3.5 31.0 - - + -
98B THR* 4.7 4.4 - - - +
99B VAL* 2.9 54.4 + - + +
101B TYR* 3.5 33.2 - + + -
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Residues in contact with LYS 47 (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 PRO* 4.8 2.4 - - - +
15B LEU* 3.7 23.3 - - + +
16B THR 5.1 1.8 + - - +
46B TRP* 1.3 73.9 - - - +
48B ASP* 1.3 62.2 + - - +
49B ARG* 3.8 34.5 + - + +
96B ASP* 4.4 9.7 + - - -
97B GLY 3.8 7.4 - - - +
98B THR* 4.1 20.0 - - - +
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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