Contacts of the strand formed by residues 43 - 58 (chain A) 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 ALA 43 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A VAL* 3.6 5.9 - - - +
42A LYS* 1.3 82.5 - - + +
44A VAL* 1.3 69.6 + - - +
45A ARG* 4.1 13.7 - - + -
75A THR* 4.7 11.0 - - + -
76A LEU 5.9 0.2 - - - -
85A GLU* 6.5 0.2 - - + -
99A TYR* 5.3 0.2 - - - -
128A PHE 4.3 0.4 - - - -
129A LEU* 3.7 0.3 - - - -
130A ASP* 2.9 45.1 + - + +
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Residues in contact with VAL 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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10A PHE* 4.6 3.6 - - + -
31A VAL* 4.0 25.4 - - + -
33A VAL* 4.3 5.8 - - + -
41A VAL* 4.4 1.1 - - + -
43A ALA* 1.3 79.1 - - - +
45A ARG* 1.3 68.1 + - - +
75A THR* 3.7 1.9 - - - +
76A LEU* 2.8 40.1 + - + +
99A TYR* 3.7 48.2 - - + +
128A PHE 3.2 8.5 - - - +
129A LEU* 3.7 22.4 - - + -
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Residues in contact with ARG 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ALA* 4.1 12.1 - - + -
44A VAL* 1.3 78.8 - - - +
46A ILE* 1.3 67.6 + - - +
74A ASP 3.3 12.8 - - - +
75A THR* 3.9 16.2 - - - +
76A LEU* 4.4 1.1 - - - +
127A ALA* 3.1 6.4 - - - +
128A PHE* 2.9 69.0 + - + +
130A ASP* 2.6 38.6 + - - +
136A THR* 4.4 9.7 + - - +
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Residues in contact with ILE 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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31A VAL* 3.9 15.7 - - + -
45A ARG* 1.3 80.8 - - - +
47A LEU* 1.3 62.6 + - - +
48A ALA* 5.3 0.9 - - + -
72A TYR* 3.8 29.6 - - + -
73A GLU* 3.2 7.6 - - - +
74A ASP* 2.8 36.9 + - + +
76A LEU* 3.7 26.4 - - + +
101A PHE* 3.5 36.6 - - + -
103A PHE* 4.6 4.3 - - + -
125A VAL* 4.1 17.5 - - + -
126A LYS 3.2 10.1 - - - +
127A ALA* 4.1 2.7 - - - -
128A PHE* 4.3 3.6 - - - -
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Residues in contact with LEU 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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46A ILE* 1.3 74.3 - - - +
48A ALA* 1.3 60.1 + - - +
49A CYS* 3.8 20.4 - - - -
71A ARG* 4.7 9.4 - - + +
72A TYR 3.2 19.3 - - - +
73A GLU* 4.1 20.6 - - + +
124A TRP* 3.7 25.9 - - + -
125A VAL* 3.4 3.1 - - - -
126A LYS* 2.8 36.2 + - - +
128A PHE* 3.6 26.9 - - + -
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Residues in contact with ALA 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ILE* 4.2 1.3 - - + +
47A LEU* 1.3 74.1 - - - +
49A CYS* 1.3 67.8 + - - +
70A LEU* 4.0 5.8 - - + +
71A ARG* 3.4 1.7 + - - -
72A TYR* 2.7 41.7 + - + +
103A PHE* 3.5 45.8 - - + -
124A TRP 3.2 7.4 - - - +
125A VAL* 4.2 5.6 - - + +
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Residues in contact with CYS 49 (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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47A LEU* 3.8 19.7 - - - -
48A ALA* 1.3 82.4 - - - +
50A GLY* 1.3 59.8 + - - +
51A VAL* 4.8 9.6 - - + -
68A GLU* 5.8 2.5 - - - -
70A LEU* 3.3 18.0 - - - +
71A ARG* 4.5 9.6 - - - -
122A ASP 3.5 1.5 - - - +
123A TYR* 3.2 5.2 - - - +
124A TRP* 2.8 75.4 + - + -
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Residues in contact with GLY 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A CYS* 1.3 73.7 - - - +
51A VAL* 1.3 59.0 + - - +
52A ALA 4.4 0.2 - - - -
68A GLU* 3.2 4.2 - - - -
69A TYR* 2.7 32.3 + - - -
70A LEU* 3.0 15.0 + - - +
122A ASP 3.1 8.1 - - - -
123A TYR* 3.6 27.8 - - - -
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Residues in contact with VAL 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A CYS* 4.8 10.8 - - + -
50A GLY* 1.3 84.1 - - - +
52A ALA* 1.3 66.0 + - - +
53A LYS* 4.1 3.5 + - + +
66A THR* 3.8 28.9 - - + -
67A SER 3.4 7.0 - - - +
68A GLU* 3.8 20.2 - - + +
69A TYR* 5.1 0.2 - - - -
70A LEU 5.3 0.2 - - - +
120A SER 4.0 0.7 - - - +
121A VAL* 3.6 3.2 - - - -
122A ASP* 2.9 41.6 + - + +
123A TYR* 4.4 0.8 - - - -
124A TRP* 5.9 4.9 - - + +
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Residues in contact with ALA 52 (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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51A VAL* 1.3 76.2 - - - +
53A LYS* 1.3 62.4 + - - +
54A VAL* 4.1 10.0 + - + +
65A GLN 4.1 0.5 - - - +
66A THR* 3.5 1.7 - - - -
67A SER* 2.7 38.7 + - - +
69A TYR* 4.0 20.5 - - + +
111A GLY* 3.4 26.9 - - - +
113A SER* 5.9 0.4 - - - +
114A PHE 5.7 1.1 - - - +
120A SER 3.2 9.6 - - - +
121A VAL* 4.5 2.0 - - + -
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Residues in contact with LYS 53 (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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51A VAL* 4.1 3.3 + - + -
52A ALA* 1.3 74.7 - - - +
54A VAL* 1.3 61.9 + - - +
55A LEU* 3.5 38.6 - - + +
64A LYS* 3.6 39.6 - - + +
65A GLN 3.6 2.9 - - - -
66A THR* 4.3 7.9 - - + +
118A TYR 3.8 0.6 - - - +
119A GLY* 3.5 2.1 - - - -
120A SER* 2.9 52.1 + - - +
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Residues in contact with VAL 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ALA* 4.1 8.5 - - + -
53A LYS* 1.3 74.6 - - - +
55A LEU* 1.3 61.4 + - - +
56A TRP* 4.1 4.2 - - + -
64A LYS* 3.2 1.7 - - - -
65A GLN* 2.7 47.6 + - + +
67A SER* 6.1 0.9 - - - +
113A SER* 5.7 2.0 - - - +
114A PHE* 4.6 27.4 - - + +
118A TYR* 3.7 9.2 - - + +
119A GLY* 4.8 2.9 - - - -
156A LEU* 4.1 24.9 - - + -
295A VAL* 3.8 30.3 - - + -
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Residues in contact with LEU 55 (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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53A LYS* 3.5 28.9 - - + +
54A VAL* 1.3 76.2 - - - +
56A TRP* 1.3 73.7 + - - +
62A GLN* 6.1 4.0 - - + -
63A CYS 3.4 8.3 - - - +
64A LYS* 3.7 30.5 - - + -
117A LYS 4.6 2.3 - - - +
118A TYR* 2.8 33.4 + - - +
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Residues in contact with TRP 56 (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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54A VAL* 4.1 10.8 - - + -
55A LEU* 1.3 89.3 - - - +
57A MET* 1.3 87.6 + - - +
58A GLN* 3.2 22.4 + - - -
62A GLN 4.1 0.3 - - - -
63A CYS* 2.7 53.1 + - + +
64A LYS* 4.7 1.3 - - - -
65A GLN 4.9 0.7 - - - -
118A TYR* 3.7 22.9 - - + -
156A LEU* 3.8 15.9 - - + -
157A MET* 3.8 22.1 - - + +
188A GLY* 3.6 3.8 - - - -
189A PHE 3.6 39.9 - - - -
190A CYS* 4.3 0.8 - - - -
295A VAL* 3.9 31.2 - - + -
297A GLY 4.0 10.3 - - - -
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Residues in contact with MET 57 (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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56A TRP* 1.3 84.7 - - - +
58A GLN* 1.3 63.2 + - - +
59A GLY 3.2 8.9 + - - +
60A SER* 3.7 27.1 - - - +
61A GLN 2.9 8.3 - - - +
62A GLN* 3.1 48.7 - - + +
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Residues in contact with GLN 58 (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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56A TRP* 3.2 25.0 + - - +
57A MET* 1.3 65.5 - - - +
59A GLY* 1.3 56.8 + - - +
60A SER 2.6 16.5 + - - -
61A GLN* 2.8 34.9 + - + +
63A CYS* 5.0 1.0 - - - +
157A MET* 4.9 5.1 - - - +
186A ARG* 3.5 45.6 + - - +
188A GLY 4.2 1.4 - - - +
190A CYS* 3.9 25.8 - - - -
193A ASP* 4.1 5.6 - - - +
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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