Contacts of the strand formed by residues 35 - 47 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A SER 3.5 0.9 - - - +
29A LEU* 3.6 2.1 - - - +
30A ASP* 2.7 34.7 + - - +
33A ALA* 3.3 27.4 - - + +
34A GLU* 1.3 81.6 - - - +
36A PHE* 1.3 60.0 + - - +
81A GLU* 3.9 14.8 - - - +
108A ARG* 2.5 37.0 + - - +
109A VAL 3.2 12.3 - - - +
110A LEU* 3.7 22.0 - - + -
111A SER 4.7 0.7 - - - +
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Residues in contact with PHE 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A CYS* 5.3 3.4 - - - -
27A TYR 4.4 1.3 - - - +
28A SER 3.5 5.6 - - - -
29A LEU* 4.0 22.0 - - + -
34A GLU 5.6 0.4 - - - -
35A THR* 1.3 78.5 - - - +
37A LYS* 1.3 75.5 + - - +
38A VAL* 4.2 14.1 - - + -
108A ARG* 3.2 6.5 - - - +
109A VAL* 2.9 67.2 + - + +
111A SER* 4.1 9.6 - - - -
125A LEU* 3.5 50.7 - - + -
126A HIS 4.3 0.4 - - - -
127A ILE* 3.9 19.3 - - + -
156A LEU* 4.9 4.9 - - + -
187A LEU* 4.7 12.1 - - + -
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Residues in contact with LYS 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A CYS* 3.5 4.3 - - - -
27A TYR* 2.9 65.6 + - + +
28A SER* 3.6 26.9 + - - +
36A PHE* 1.3 88.5 - - - +
38A VAL* 1.3 60.9 + - - +
107A ALA 3.7 4.9 - - - +
108A ARG* 3.9 35.2 - - + +
81C GLU* 4.0 10.7 + - + -
82C ASN* 5.5 10.4 + - - +
108C ARG* 5.6 2.6 - - - +
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Residues in contact with VAL 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LEU* 3.6 30.7 - - + -
25A GLU 3.4 8.7 - - - +
26A CYS* 4.3 5.2 - - - -
27A TYR* 4.6 4.2 + - - -
36A PHE* 4.2 12.0 + - + -
37A LYS* 1.3 75.6 - - - +
39A ASN* 1.3 63.8 + - - +
40A ALA* 4.0 10.3 - - + -
105A PHE* 3.8 23.1 - - + +
106A SER* 3.4 2.9 - - - -
107A ALA 2.9 40.8 + - - +
109A VAL* 4.1 19.1 - - + -
127A ILE* 4.3 9.2 - - + -
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Residues in contact with ASN 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ILE* 2.9 9.3 + - - +
25A GLU* 2.8 50.4 + - + +
27A TYR* 4.3 1.3 - - - +
38A VAL* 1.3 74.8 - - - +
40A ALA* 1.3 61.8 + - - +
104A ARG* 2.6 44.9 + - - +
105A PHE 2.7 31.8 + - - -
106A SER* 3.8 9.6 - - - -
78C VAL 4.6 0.2 - - - +
80C VAL* 3.7 11.4 - - - +
81C GLU 4.0 14.8 - - - +
82C ASN* 5.8 1.8 - - - -
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Residues in contact with ALA 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ILE* 3.8 7.9 - - + -
22A TYR 3.1 20.6 - - - +
23A LEU* 3.8 6.7 - - - -
24A ILE* 4.0 5.2 - - - +
38A VAL* 4.0 7.8 - - + -
39A ASN* 1.3 76.3 - - - +
41A PHE* 1.3 60.7 + - - +
104A ARG* 3.1 11.8 - - - +
105A PHE* 2.9 57.2 + - + -
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Residues in contact with PHE 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A GLY 3.5 0.4 - - - +
21A ILE* 3.0 13.3 - - - +
22A TYR* 2.9 58.0 + + + -
24A ILE* 4.2 11.2 - - + -
40A ALA* 1.3 76.9 - - - +
42A LEU* 1.3 59.2 + - - +
89A VAL* 3.9 21.5 - - + -
102A LEU* 3.6 28.5 - - + -
103A GLU 3.0 19.1 - - - -
104A ARG* 4.0 11.9 - - + -
105A PHE* 4.0 2.2 - - - -
76C ARG* 3.5 26.5 - - - -
130C ILE* 6.1 0.9 - - + -
132C ARG* 5.1 2.7 - - - -
175C LEU* 3.9 22.0 - - + -
176C GLU* 4.2 9.0 - - - +
180C GLU* 4.0 9.4 - - - -
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Residues in contact with LEU 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A GLY 3.3 19.7 - - - +
21A ILE* 4.0 9.2 - - + -
41A PHE* 1.3 73.1 - - - +
43A SER* 1.3 63.3 + - - +
44A LEU* 4.1 20.8 + - + -
75A ILE* 4.3 23.3 - - + -
77A PHE* 4.6 9.0 - - + -
84A ARG* 4.0 12.8 - - - +
101A TYR* 4.1 2.2 - - + +
102A LEU* 3.5 5.0 - - - +
103A GLU* 2.9 65.7 + - + +
105A PHE* 4.0 11.1 - - + -
129A LEU* 3.8 23.8 - - + -
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Residues in contact with SER 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ASN 2.9 13.3 - - - +
19A THR* 3.1 2.4 - - - -
20A GLY 2.8 31.8 + - - -
41A PHE 4.9 0.5 + - - -
42A LEU* 1.3 73.7 + - - +
44A LEU* 1.3 63.1 + - - +
101A TYR 3.7 5.6 - - - -
102A LEU* 3.6 3.4 - - - +
146A GLU* 3.3 26.2 - - - +
176C GLU* 2.9 34.5 + - - -
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Residues in contact with LEU 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A VAL* 3.7 25.4 - - + -
18A ASN 3.2 4.5 - - - -
19A THR* 4.0 20.6 - - + -
42A LEU* 4.1 17.4 - - + -
43A SER* 1.3 77.1 - - - +
45A SER* 1.3 61.4 + - - +
46A TRP* 4.3 4.5 - - + -
72A ILE* 5.1 1.1 - - + -
73A PRO* 4.4 17.7 - - + +
75A ILE* 3.4 35.0 - - + -
100A GLN* 4.0 1.0 - - - +
101A TYR* 2.8 65.7 + - + +
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Residues in contact with SER 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A VAL* 3.8 0.9 - - - -
18A ASN* 3.0 53.6 + - - +
44A LEU* 1.3 75.1 - - - +
46A TRP* 1.3 64.8 + - - +
98A THR* 4.9 5.5 - - - +
99A VAL 3.1 8.3 - - - -
100A GLN* 3.4 26.5 - - - -
143A VAL* 5.2 1.2 - - - +
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Residues in contact with TRP 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A LEU* 4.2 13.0 - - + -
16A THR 4.1 14.6 - - - +
17A VAL* 4.6 8.1 - - + -
18A ASN* 5.6 0.4 - - - +
44A LEU* 4.2 7.4 - - + -
45A SER* 1.3 84.6 - - - +
47A LYS* 1.3 74.4 + - - +
48A ASP* 3.5 17.6 + - + +
70A ILE* 4.1 1.3 - - + -
71A TRP* 3.2 43.6 + + - -
72A ILE* 3.6 25.6 - - + -
73A PRO* 3.7 27.8 - - + -
98A THR* 4.3 5.3 - - - +
99A VAL* 2.8 60.9 + - + +
101A TYR* 3.5 25.8 - - + -
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Residues in contact with LYS 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A PRO* 4.8 3.5 - - - +
15A LEU* 3.6 24.1 - - + +
16A THR 5.5 3.1 - - - +
46A TRP* 1.3 74.8 - - - +
48A ASP* 1.3 61.0 + - - +
49A ARG* 3.8 32.0 + - + +
96A ASP* 5.3 5.4 - - - +
97A GLY 3.4 7.2 - - - +
98A THR* 4.0 16.6 - - - +
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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