Contacts of the strand formed by residues 119 - 130 (chain C) in PDB entry 4LL1
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 GLY 119 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53C LYS* 3.2 10.1 - - - -
55C LEU* 4.2 10.5 + - - +
114C PHE* 3.2 24.6 - - - -
116C GLY 3.4 15.2 + - - -
117C LYS 3.2 8.1 + - - -
118C TYR* 1.3 74.6 - - - +
120C SER* 1.3 61.2 + - - -
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Residues in contact with SER 120 (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 4.0 0.7 + - - +
52C ALA* 3.2 1.9 - - - -
53C LYS* 2.8 52.0 + - - +
114C PHE* 3.3 12.8 - - - -
115C LYS* 3.9 25.0 + - - -
119C GLY* 1.3 73.9 - - - -
121C VAL* 1.3 66.6 + - - +
122C ASP* 3.7 11.4 + - - -
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Residues in contact with VAL 121 (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 3.4 10.3 - - - +
52C ALA* 3.4 21.3 - - + -
54C VAL* 6.5 0.4 - - + -
69C TYR* 4.9 1.1 - - + -
111C GLY* 3.8 8.3 - - - +
112C THR 2.9 36.3 - - - +
113C SER* 3.7 5.6 - - - +
114C PHE* 2.8 29.9 + - + +
115C LYS* 4.2 0.9 - - - +
120C SER* 1.3 78.2 - - - +
122C ASP* 1.3 69.7 + - - +
123C TYR* 3.7 26.9 - - + +
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Residues in contact with ASP 122 (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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49C CYS 3.8 1.0 - - - +
50C GLY* 3.3 1.4 - - - -
51C VAL* 2.9 42.7 + - + +
53C LYS* 5.2 4.3 + - - -
113C SER* 5.4 0.9 - - - -
115C LYS* 2.5 40.1 + - - -
120C SER* 3.7 14.1 + - - -
121C VAL* 1.3 77.3 - - - +
123C TYR* 1.3 63.8 + - - +
124C TRP* 4.1 20.2 - - + +
142C ASN* 5.2 4.7 - - - +
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Residues in contact with TYR 123 (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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49C CYS 3.2 4.7 - - - -
50C GLY* 3.4 21.3 - - - -
69C TYR* 3.2 27.3 - + + +
70C LEU* 4.1 16.2 - - + -
105C LEU* 4.5 7.4 - - + -
110C LEU* 3.2 23.9 - - + +
111C GLY 3.5 17.0 + - - -
113C SER* 4.0 8.9 + - - -
121C VAL* 3.7 16.4 - - + -
122C ASP* 1.3 76.5 - - - +
124C TRP* 1.3 64.4 + - - +
142C ASN* 3.2 7.4 + - - +
143C PHE* 3.0 59.0 + + + +
145C VAL* 3.6 32.1 - - + -
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Residues in contact with TRP 124 (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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47C LEU* 3.7 20.4 - - + -
48C ALA* 3.4 2.4 - - - -
49C CYS* 3.0 64.9 + - + +
51C VAL* 5.1 8.7 - - + +
122C ASP* 4.1 21.7 + - + +
123C TYR* 1.3 80.9 - - - +
125C VAL* 1.3 64.5 + - - +
126C LYS* 3.6 52.7 - - + -
140C LYS* 3.8 30.2 - - + +
141C LYS 3.3 12.6 - - - +
142C ASN* 3.5 18.2 - - - +
143C PHE* 3.6 8.3 - - - -
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Residues in contact with VAL 125 (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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12C VAL* 4.2 19.7 - - + +
14C PHE* 3.6 33.7 - - + -
46C ILE* 4.0 31.4 - - + -
47C LEU 3.4 6.7 - - - +
48C ALA* 4.2 1.3 - - + -
101C PHE* 4.3 8.1 - - + -
103C PHE* 3.8 28.5 - - + -
124C TRP* 1.3 80.2 - - - +
126C LYS* 1.3 63.3 + - - +
139C THR 4.0 0.3 - - - +
140C LYS* 3.4 1.9 - - - +
141C LYS 2.8 32.0 + - - -
143C PHE* 4.0 1.6 - - + -
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Residues in contact with LYS 126 (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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46C ILE* 3.1 4.0 - - - +
47C LEU* 2.6 43.2 + - + +
124C TRP* 3.6 35.4 - - + -
125C VAL* 1.3 75.0 - - - +
127C ALA* 1.3 59.5 + - - +
128C PHE* 3.7 22.1 - - + -
138C GLU* 3.8 28.8 + - - +
139C THR 3.2 9.9 - - - +
140C LYS* 3.6 37.9 - - + +
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Residues in contact with ALA 127 (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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10C PHE* 3.6 19.3 - - + -
12C VAL* 3.9 14.9 - - + +
31C VAL* 3.9 20.0 - - + -
44C VAL* 5.1 0.4 - - + -
45C ARG 3.2 8.7 - - - +
46C ILE* 4.2 1.8 - - + -
125C VAL 4.2 0.6 - - - -
126C LYS* 1.3 72.4 - - - +
128C PHE* 1.3 62.9 + - - +
138C GLU* 3.4 4.7 - - - +
139C THR* 2.8 44.6 + - + +
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Residues in contact with PHE 128 (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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10C PHE* 3.9 2.5 - - - -
44C VAL* 3.4 6.9 - - - +
45C ARG* 2.7 89.0 + - + +
46C ILE 3.9 1.1 - - - -
47C LEU* 3.5 44.9 - - + -
73C GLU* 5.1 3.8 - - - -
126C LYS* 3.7 19.3 - - + -
127C ALA* 1.3 72.5 - - - +
129C LEU* 1.3 62.2 + - - +
130C ASP* 3.8 1.6 + - - +
136C THR* 5.3 4.9 - - - -
137C GLN 3.3 7.4 - - - +
138C GLU* 3.7 36.8 - - + -
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Residues in contact with LEU 129 (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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10C PHE* 3.6 25.6 - - + -
33C VAL* 4.2 24.2 - - + -
35C VAL* 6.4 1.1 - - + -
41C VAL* 3.6 26.9 - - + -
43C ALA 3.6 15.0 - - - +
44C VAL* 3.7 13.5 - - + -
91C MET* 5.3 0.4 - - - -
128C PHE* 1.3 71.6 - - - +
130C ASP* 1.3 62.6 + - - +
131C ARG* 3.8 22.6 + - - +
136C THR* 3.4 5.9 - - - -
137C GLN* 2.9 49.7 + - + +
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Residues in contact with ASP 130 (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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41C VAL* 3.7 2.9 - - - +
42C LYS* 3.1 34.6 + - + +
43C ALA* 3.0 38.3 + - + +
45C ARG* 2.7 48.2 + - - -
128C PHE 3.8 0.6 + - - -
129C LEU* 1.3 73.7 - - - +
131C ARG* 1.3 66.2 + - - +
136C THR* 3.0 19.9 - - + +
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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