Contacts of the strand formed by residues 35 - 47 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C SER 3.6 0.5 - - - +
29C LEU* 3.5 2.9 - - - +
30C ASP* 2.6 34.4 + - - +
33C ALA* 3.3 24.8 - - + +
34C GLU* 1.3 80.4 - - - +
36C PHE* 1.3 58.9 + - - +
81C GLU* 3.2 31.2 - - - +
108C ARG* 2.1 39.7 + - - -
109C VAL 3.2 12.1 - - - -
110C LEU* 3.5 11.4 - - + +
111C SER 4.4 1.1 - - - +
113C LEU* 5.4 0.2 - - - +
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Residues in contact with PHE 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C CYS* 5.2 3.4 - - - -
27C TYR 4.3 1.6 - - - +
28C SER 3.4 7.4 - - - -
29C LEU* 3.8 23.1 - - + -
35C THR* 1.3 76.9 - - - +
37C LYS* 1.3 82.0 + - - +
38C VAL* 4.2 8.7 - - + -
108C ARG* 3.3 8.0 - - - +
109C VAL* 2.9 62.6 + - + +
111C SER* 4.1 7.6 - - - -
125C LEU* 3.5 45.5 - - + -
126C HIS 4.0 2.9 - - - -
127C ILE* 3.7 28.7 - - + -
156C LEU* 5.1 5.2 - - + -
187C LEU* 4.6 15.7 - - + -
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Residues in contact with LYS 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B GLU* 4.5 6.4 + - - +
82B ASN* 6.2 1.8 - - - +
108B ARG* 6.1 1.0 - - - +
26C CYS* 3.7 4.2 - - - -
27C TYR* 2.9 68.3 + - + +
28C SER* 3.6 25.0 + - - +
36C PHE* 1.3 86.7 - - - +
38C VAL* 1.3 61.4 + - - +
107C ALA 3.6 5.2 - - - +
108C ARG* 3.7 39.4 - - + +
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Residues in contact with VAL 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C LEU* 3.8 28.9 - - + -
25C GLU 3.8 6.5 - - - +
26C CYS* 4.4 7.2 - - - +
27C TYR* 4.4 4.1 + - - -
36C PHE* 4.2 6.7 - - + -
37C LYS* 1.3 75.9 - - - +
39C ASN* 1.3 63.4 + - - +
40C ALA* 4.3 8.7 - - + -
77C PHE* 5.0 0.2 - - + -
105C PHE* 3.8 22.6 - - + +
106C SER* 3.3 2.9 - - - -
107C ALA* 2.9 43.4 + - + +
108C ARG* 4.7 0.2 - - - +
109C VAL* 3.8 20.2 - - + -
127C ILE* 4.0 17.3 - - + -
187C LEU* 6.2 0.2 - - + -
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Residues in contact with ASN 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B VAL* 3.3 21.0 + - - +
81B GLU 3.9 17.1 + - - +
82B ASN 5.5 2.4 + - - -
23C LEU* 4.3 0.3 - - - -
24C ILE* 2.9 6.9 + - - +
25C GLU* 2.9 52.9 + - + +
27C TYR* 4.0 2.9 - - + -
38C VAL* 1.3 75.1 - - - +
40C ALA* 1.3 60.8 + - - +
104C ARG* 3.1 40.1 + - - +
105C PHE 3.0 19.9 - - - +
106C SER* 3.8 4.4 - - - -
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Residues in contact with ALA 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C ILE* 3.7 16.6 - - + -
22C TYR 3.2 15.3 - - - +
23C LEU* 3.8 11.7 - - + -
24C ILE* 3.6 9.6 - - - -
38C VAL* 4.2 2.0 - - + -
39C ASN* 1.3 76.5 + - - +
41C PHE* 1.3 60.8 + - - +
104C ARG* 3.1 8.1 - - - +
105C PHE* 2.9 54.4 + - + -
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Residues in contact with PHE 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B ARG* 3.2 32.1 - - - -
130B ILE* 5.6 2.0 - - + -
132B ARG* 5.0 2.7 - - - -
175B LEU* 3.6 19.3 - - + -
176B GLU* 4.6 5.6 - - - +
180B GLU* 3.5 18.4 - - - -
21C ILE* 3.2 11.6 - - - +
22C TYR* 2.9 52.5 + + + +
24C ILE* 3.9 16.4 - - + -
40C ALA* 1.3 75.3 - - - +
42C LEU* 1.3 59.6 + - - +
43C SER 4.1 0.4 - - - -
89C VAL* 3.8 24.7 - - + -
102C LEU* 3.6 26.7 - - + -
103C GLU 3.3 15.3 - - - -
104C ARG* 4.1 7.4 - - + -
105C PHE* 4.0 1.3 - - - -
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Residues in contact with LEU 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C GLY 3.2 18.2 - - - +
21C ILE* 3.9 11.0 - - + -
40C ALA 4.1 0.8 + - - -
41C PHE* 1.3 73.7 - - - +
43C SER* 1.3 61.1 + - - +
44C LEU* 4.1 27.5 + - + -
75C ILE* 4.4 14.1 - - + -
77C PHE* 4.2 21.3 - - + -
84C ARG* 4.3 4.9 - - - +
101C TYR* 3.9 1.6 - - - +
102C LEU* 3.3 6.1 - - - +
103C GLU* 2.9 62.2 + - + +
105C PHE* 4.0 10.9 - - + -
129C LEU* 3.8 23.3 - - + -
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Residues in contact with SER 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176B GLU* 2.9 34.8 + - - -
18C ASN 3.1 1.9 - - - +
19C THR* 3.1 8.9 - - - -
20C GLY 2.7 35.3 + - - -
41C PHE* 5.0 0.7 - - - +
42C LEU* 1.3 71.3 + - - +
44C LEU* 1.3 62.8 + - - +
101C TYR 3.7 5.2 - - - -
102C LEU* 3.5 7.5 - - - +
146C GLU* 3.5 24.2 - - - -
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Residues in contact with LEU 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C VAL* 4.3 9.2 - - + -
18C ASN 3.3 2.7 - - - -
19C THR* 4.0 24.0 - - + -
42C LEU* 4.1 23.1 - - + -
43C SER* 1.3 82.2 - - - +
45C SER* 1.3 61.8 + - - +
46C TRP* 4.2 8.1 - - + -
72C ILE* 5.3 0.4 - - + -
73C PRO* 4.8 11.4 - - + +
75C ILE* 3.6 36.6 - - + -
84C ARG* 6.1 0.9 - - - +
100C GLN* 4.0 0.9 - - - +
101C TYR* 2.8 67.8 + - + +
103C GLU* 6.1 0.2 - - - -
129C LEU* 5.6 0.2 - - + -
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Residues in contact with SER 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C THR 3.8 1.4 - - - +
17C VAL* 3.6 1.5 - - - +
18C ASN* 2.9 53.7 + - - +
44C LEU* 1.3 75.8 - - - +
46C TRP* 1.3 66.1 + - - +
98C THR* 5.3 4.3 - - - -
99C VAL 3.1 14.1 - - - -
100C GLN* 3.8 18.8 - - - -
143C VAL* 5.5 1.2 - - - +
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Residues in contact with TRP 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C PRO* 5.1 0.2 - - + -
15C LEU* 4.7 9.0 - - + -
16C THR 3.6 16.6 - - - +
17C VAL* 4.4 9.6 - - + -
18C ASN* 5.9 0.4 - - - +
44C LEU* 4.2 8.7 - - + -
45C SER* 1.3 83.1 - - - +
47C LYS* 1.3 72.7 + - - +
48C ASP* 3.6 11.8 + - + +
70C ILE* 4.3 5.3 - - + +
71C TRP* 3.4 41.0 + + - -
72C ILE* 4.2 12.8 - - + -
73C PRO* 3.5 33.9 - - + -
98C THR* 4.7 4.2 - - - +
99C VAL* 2.9 65.5 + - + +
101C TYR* 3.6 28.7 - + + -
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Residues in contact with LYS 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C PRO* 4.7 2.8 - - - +
15C LEU* 3.7 24.4 - - + +
16C THR* 4.7 5.7 + - - +
46C TRP* 1.3 75.0 - - - +
48C ASP* 1.3 61.3 + - - +
49C ARG* 3.7 34.5 + - - +
96C ASP* 5.5 3.8 - - - +
97C GLY 3.4 9.4 - - - +
98C THR* 4.4 13.5 - - - +
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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
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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