Contacts of the strand formed by residues 35 - 47 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28D SER 3.5 1.4 + - - +
29D LEU* 3.5 2.2 - - - +
30D ASP* 2.7 36.1 + - - +
33D ALA* 3.4 23.8 - - + +
34D GLU* 1.3 83.8 - - - +
36D PHE* 1.3 60.5 + - - +
81D GLU* 3.9 15.5 - - - +
108D ARG* 2.4 34.0 + - - +
109D VAL 3.4 11.0 - - - -
110D LEU* 3.8 21.8 - - + -
111D SER 4.7 0.4 - - - +
113D LEU* 5.1 0.4 - - - +
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Residues in contact with PHE 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D CYS* 4.9 12.8 - - - -
27D TYR 4.3 2.5 - - - +
28D SER 3.4 7.4 - - - -
29D LEU* 3.8 23.6 - - + -
34D GLU 6.2 0.2 - - - -
35D THR* 1.3 76.9 - - - +
37D LYS* 1.3 73.5 + - - +
38D VAL* 4.3 12.8 - - + -
108D ARG* 3.4 6.6 - - - +
109D VAL* 2.9 72.6 + - + +
111D SER* 4.2 8.3 - - - -
125D LEU* 3.6 50.9 - - + -
127D ILE* 4.0 13.2 - - + -
156D LEU* 5.2 3.6 - - + -
187D LEU* 5.0 4.7 - - + -
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Residues in contact with LYS 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A GLU* 4.5 9.9 + - - -
82A ASN* 6.2 1.3 - - - +
26D CYS* 3.9 3.8 - - - -
27D TYR* 3.2 66.1 + - + +
28D SER* 4.2 16.5 + - - +
36D PHE* 1.3 86.5 - - - +
38D VAL* 1.3 62.1 + - - +
107D ALA 3.7 5.2 - - - +
108D ARG* 3.7 41.4 - - + +
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Residues in contact with VAL 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D LEU* 3.5 32.1 - - + -
25D GLU 3.7 10.1 - - - +
26D CYS* 4.6 5.6 - - - -
27D TYR* 4.5 4.6 + - - -
36D PHE* 4.3 11.6 - - + -
37D LYS* 1.3 75.0 - - - +
39D ASN* 1.3 64.2 + - - +
40D ALA* 4.1 9.6 - - + -
105D PHE* 4.0 21.9 - - + +
106D SER* 3.4 2.4 - - - -
107D ALA* 2.9 38.6 + - + +
108D ARG* 4.7 0.2 - - - +
109D VAL* 3.8 23.5 - - + +
127D ILE* 4.0 9.2 - - + -
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Residues in contact with ASN 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A VAL* 3.7 10.2 - - - +
81A GLU 3.9 20.1 - - - +
82A ASN 5.5 3.0 - - - +
24D ILE* 2.9 24.4 + - - +
25D GLU* 3.0 23.2 + - + +
27D TYR* 4.2 8.2 - - + +
38D VAL* 1.3 73.4 - - - +
40D ALA* 1.3 61.4 + - - +
104D ARG* 2.6 43.5 + - - +
105D PHE 2.8 26.0 + - - -
106D SER* 3.5 5.9 - - - -
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Residues in contact with ALA 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D ILE* 4.0 8.5 - - + -
22D TYR 3.1 22.2 - - - +
23D LEU* 3.7 7.0 - - - -
24D ILE* 4.0 4.3 - - - +
38D VAL* 4.1 7.4 - - + -
39D ASN* 1.3 75.7 - - - +
41D PHE* 1.3 62.2 + - - +
104D ARG* 3.2 11.2 - - - +
105D PHE* 2.9 56.4 + - + -
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Residues in contact with PHE 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A ARG* 3.8 25.8 - - - -
130A ILE* 6.0 1.3 - - + -
132A ARG* 5.1 1.6 - - - -
175A LEU* 3.8 25.6 - - + -
176A GLU* 4.1 14.1 - - - +
180A GLU* 4.2 6.7 - - - -
20D GLY 3.6 0.2 - - - +
21D ILE* 3.2 12.8 - - - +
22D TYR* 2.9 57.8 + + + +
24D ILE* 4.3 12.6 - - + -
40D ALA* 1.3 76.8 - - - +
42D LEU* 1.3 58.5 + - - +
89D VAL* 3.8 19.3 - - + -
102D LEU* 3.4 33.2 - - + -
103D GLU 3.1 15.5 - - - -
104D ARG* 4.1 10.3 - - + -
105D PHE* 3.9 3.6 - - - -
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Residues in contact with LEU 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D GLY 3.5 16.8 - - - +
21D ILE* 4.4 8.1 - - + -
41D PHE* 1.3 72.6 - - - +
43D SER* 1.3 61.7 - - - +
44D LEU* 4.1 20.6 + - + -
75D ILE* 4.1 22.0 - - + -
77D PHE* 4.4 11.4 - - + -
84D ARG* 4.1 16.8 - - - +
101D TYR* 4.1 1.2 - - - +
102D LEU* 3.3 6.1 - - - +
103D GLU* 3.0 62.2 + - + +
105D PHE* 3.9 10.5 - - + -
129D LEU* 3.7 24.9 - - + -
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Residues in contact with SER 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A GLU* 2.7 36.2 + - - -
18D ASN 3.3 1.6 - - - +
19D THR* 3.1 9.4 - - - -
20D GLY* 2.8 39.6 + - - -
41D PHE* 4.7 1.2 - - - +
42D LEU* 1.3 75.4 - - - +
44D LEU* 1.3 62.4 + - - +
101D TYR 3.8 4.3 - - - -
102D LEU* 4.0 1.6 - - - +
146D GLU* 3.7 22.1 - - - +
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Residues in contact with LEU 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D VAL* 3.9 18.4 - - + -
18D ASN 3.3 1.3 - - - -
19D THR* 3.9 18.2 - - + -
42D LEU* 4.1 16.8 - - + -
43D SER* 1.3 80.7 - - - +
45D SER* 1.3 62.1 + - - +
46D TRP* 4.0 7.9 - - + -
72D ILE* 5.1 1.6 - - + -
73D PRO* 4.6 18.2 - - + +
75D ILE* 3.7 30.7 - - + -
100D GLN* 3.8 1.9 - - - +
101D TYR* 2.9 70.5 + - + +
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Residues in contact with SER 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D THR 3.9 1.2 - - - +
17D VAL* 3.8 0.7 - - - -
18D ASN* 2.9 51.0 + - - +
44D LEU* 1.3 76.7 - - - +
46D TRP* 1.3 64.8 + - - +
98D THR* 5.3 4.0 - - - -
99D VAL 3.2 8.3 - - - -
100D GLN* 3.5 22.4 - - - -
143D VAL* 5.7 0.2 - - - +
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Residues in contact with TRP 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D LEU* 4.1 10.8 - - + -
16D THR 3.6 17.5 - - - +
17D VAL* 4.4 8.7 - - + -
18D ASN* 6.0 0.2 - - - +
44D LEU* 4.0 7.2 - - + -
45D SER* 1.3 86.2 - - - +
47D LYS* 1.3 70.8 + - - +
48D ASP* 4.1 7.1 - - + +
70D ILE* 4.5 0.9 - - + -
71D TRP* 3.1 47.6 + + - -
72D ILE* 4.1 14.6 - - + -
73D PRO* 3.5 33.2 - - + -
98D THR* 4.7 3.5 - - - +
99D VAL* 2.8 66.3 + - + +
101D TYR* 3.6 29.8 - + + -
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Residues in contact with LYS 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D PRO* 4.7 2.6 - - - +
15D LEU* 3.5 24.7 - - + +
16D THR 4.7 1.5 + - - +
46D TRP* 1.3 75.3 - - - +
48D ASP* 1.3 60.4 + - - +
49D ARG* 3.8 35.1 + - + +
96D ASP* 4.6 17.2 + - - +
97D GLY* 3.2 13.0 - - - +
98D THR* 4.3 13.9 - - - +
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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