Contacts of the strand formed by residues 43 - 58 (chain C) in PDB entry 4LL4
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 ALA 43 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C VAL* 3.3 13.0 - - - +
42C LYS* 1.3 84.6 - - + +
44C VAL* 1.3 61.2 + - - +
45C ARG* 4.1 9.9 - - + +
75C THR* 4.5 16.4 - - + -
85C GLU 5.8 0.9 - - - +
89C VAL* 6.0 0.7 - - - -
129C LEU* 3.9 0.5 - - - -
130C ASP* 3.2 43.6 + - - +
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Residues in contact with VAL 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C PHE* 4.8 3.6 - - + -
31C VAL* 4.6 13.0 - - + -
33C VAL* 4.7 9.0 - - + -
41C VAL* 4.4 4.0 - - + +
43C ALA* 1.3 76.3 - - - +
45C ARG* 1.3 59.9 + - - +
75C THR* 3.5 4.9 - - - +
76C LEU* 2.8 49.0 + - + +
91C MET* 5.5 1.6 - - + -
99C TYR* 3.8 54.1 + - + +
128C PHE 3.9 6.3 - - - +
129C LEU* 4.1 21.8 - - + -
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Residues in contact with ARG 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ALA* 4.1 7.5 - - + +
44C VAL* 1.3 75.0 - - - +
46C ILE* 1.3 68.8 + - - +
73C GLU* 4.5 16.8 + - + +
74C ASP 3.6 14.4 - - - +
75C THR* 4.0 22.0 - - + +
76C LEU* 5.1 0.7 - - - -
127C ALA* 3.4 2.8 - - - +
128C PHE* 3.0 73.0 + - + +
130C ASP* 3.0 39.5 + - - -
136C THR* 3.8 14.3 + - - +
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Residues in contact with ILE 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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31C VAL* 4.1 14.6 - - + -
45C ARG* 1.3 81.8 - - - +
47C LEU* 1.3 61.2 + - - +
48C ALA* 5.2 1.8 - - + -
72C TYR* 4.2 22.7 - - + +
73C GLU* 3.4 5.0 - - - +
74C ASP* 2.8 50.0 + - + +
76C LEU* 3.9 26.2 - - + +
101C PHE* 3.8 34.8 - - + -
103C PHE* 4.8 3.8 - - + -
125C VAL* 4.2 16.4 - - + -
126C LYS 3.0 13.7 - - - +
127C ALA* 4.1 5.6 - - + -
128C PHE* 4.2 4.0 - - - -
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Residues in contact with LEU 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C ILE* 1.3 76.5 - - - +
48C ALA* 1.3 57.1 + - - +
49C CYS* 3.4 32.8 - - - -
71C ARG* 4.6 9.0 - - + -
72C TYR 3.3 25.8 - - - +
73C GLU* 4.3 21.8 - - + +
124C TRP* 3.8 11.6 - - + -
125C VAL* 3.5 0.5 - - - +
126C LYS* 2.6 43.5 + - + +
128C PHE* 3.7 25.8 - - + -
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Residues in contact with ALA 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C ILE* 5.2 1.3 - - + -
47C LEU* 1.3 74.1 - - - +
49C CYS* 1.3 63.6 + - - +
70C LEU* 3.1 21.4 - - + +
72C TYR* 2.9 32.2 + - + +
103C PHE* 3.8 23.6 - - + -
124C TRP 3.4 6.5 - - - +
125C VAL* 3.7 24.5 - - + -
143C PHE* 5.2 0.2 - - + -
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Residues in contact with CYS 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C LEU* 3.4 29.4 - - - -
48C ALA* 1.3 74.0 - - - +
50C GLY* 1.3 63.1 + - - +
51C VAL* 4.9 5.8 - - + -
68C GLU* 5.7 4.0 - - + +
70C LEU* 3.1 14.1 - - - +
71C ARG* 5.1 5.8 - - - -
122C ASP 3.8 0.8 - - - +
123C TYR* 3.0 25.2 - - - +
124C TRP* 3.1 53.1 + - + +
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Residues in contact with GLY 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C CYS* 1.3 76.0 - - - +
51C VAL* 1.3 65.4 + - - +
68C GLU* 3.4 5.5 - - - +
69C TYR* 2.9 28.2 + - - -
70C LEU* 3.1 12.2 + - - +
122C ASP 3.2 7.6 - - - -
123C TYR* 3.4 24.5 - - - -
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Residues in contact with VAL 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C CYS* 4.9 9.2 - - + -
50C GLY* 1.3 79.5 - - - +
52C ALA* 1.3 74.9 + - - +
53C LYS* 4.7 20.4 - - + +
66C THR* 4.1 16.6 - - + -
67C SER 3.2 11.2 - - - +
68C GLU* 4.5 10.3 - - + +
69C TYR* 4.7 0.7 - - - -
120C CYS 4.0 0.5 - - - +
121C VAL* 3.2 8.4 - - - +
122C ASP* 2.9 41.7 + - - +
124C TRP* 5.1 7.9 - - + +
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Residues in contact with ALA 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C VAL* 1.3 79.3 - - - +
53C LYS* 1.3 63.8 + - - +
54C VAL* 4.1 8.7 - - + -
65C GLN 4.4 0.4 - - - -
66C THR* 3.3 4.9 - - - -
67C SER* 2.7 40.7 + - - +
69C TYR* 3.9 22.6 - - + +
111C GLY* 4.8 2.2 - - - -
120C CYS 3.3 9.6 - - - +
121C VAL* 4.0 14.1 - - + +
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Residues in contact with LYS 53 (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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51C VAL* 4.4 21.9 + - + +
52C ALA* 1.3 76.3 - - - +
54C VAL* 1.3 65.3 + - - +
55C LEU* 5.4 5.4 - - + -
64C LYS* 4.1 23.3 - - + +
65C GLN 3.5 4.9 - - - +
66C THR* 4.1 17.0 - - + +
118C TYR 3.4 0.2 - - - +
119C GLY* 3.4 7.4 - - - -
120C CYS* 3.0 45.4 + - - +
122C ASP* 5.0 7.5 + - - +
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Residues in contact with VAL 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C ALA* 5.1 8.5 - - + -
53C LYS* 1.3 75.2 - - - +
55C LEU* 1.3 62.6 + - - +
56C TRP* 4.4 3.8 - - + -
64C LYS* 3.3 5.9 - - - +
65C GLN* 2.8 44.5 + - + +
67C SER* 6.0 1.8 - - - +
118C TYR* 3.2 15.3 - - + +
156C LEU* 3.7 29.6 - - + -
295C VAL* 4.2 27.8 - - + -
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Residues in contact with LEU 55 (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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53C LYS* 4.9 7.2 - - + +
54C VAL* 1.3 76.7 - - - +
56C TRP* 1.3 61.8 + - - +
62C GLN* 3.0 37.7 - - + +
63C CYS 3.5 5.2 - - - -
64C LYS* 3.9 35.7 - - + +
117C LYS 4.8 0.2 - - - +
118C TYR* 3.1 36.1 + - - +
119C GLY* 5.1 3.8 - - - +
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Residues in contact with TRP 56 (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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54C VAL 4.4 8.1 - - - -
55C LEU* 1.3 85.6 - - - +
57C MET* 1.3 89.0 + - - +
58C GLN* 2.8 22.5 + - + -
62C GLN* 3.3 5.7 - - - +
63C CYS* 2.8 69.5 + - + -
65C GLN 4.6 0.9 - - - -
118C TYR* 3.6 23.3 - - + -
156C LEU* 4.0 16.4 - - + -
157C MET* 4.2 17.1 - - + +
188C GLY* 3.8 4.7 - - - -
189C PHE 3.4 40.4 - - - -
190C CYS* 4.1 3.2 - - - -
295C VAL* 3.7 26.2 - - + -
297C GLY* 3.6 17.0 - - - -
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Residues in contact with MET 57 (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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56C TRP* 1.3 87.3 - - - +
58C GLN* 1.3 63.6 + - - +
59C GLY 3.6 23.1 + - - +
60C SER 3.7 11.4 - - - +
61C GLN 3.5 17.3 - - - -
62C GLN* 3.9 24.2 - - + +
157C MET* 5.5 2.4 - - - +
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Residues in contact with GLN 58 (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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56C TRP* 2.8 26.3 + - - +
57C MET* 1.3 74.0 + - - +
59C GLY* 1.3 63.5 + - - +
60C SER 3.2 2.8 + - - -
61C GLN* 2.7 26.6 + - + +
63C CYS* 4.1 1.1 - - - -
157C MET* 4.8 5.9 - - - -
186C ARG* 2.5 45.1 + - - +
188C GLY 3.8 0.2 - - - +
190C CYS* 3.4 29.3 - - - -
193C ASP* 3.9 10.3 - - - +
299C ARG* 5.5 3.3 + - - +
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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
------------------------------------------------------------
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