Contacts of the helix formed by residues 42 - 52 (chain A) in PDB entry 3LL8
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 ARG 42 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A LYS 2.5 30.5 + - - -
33A GLU* 3.0 16.3 + - - +
34A VAL* 2.7 19.3 + - - +
36A ASP* 3.1 52.0 + - + +
40A LYS 4.6 0.9 - - - +
41A PRO* 1.3 71.8 - - - +
43A VAL* 1.3 63.7 + - - +
44A ASP* 3.2 14.1 - - - +
45A ILE* 3.3 33.3 + - + +
46A LEU* 3.1 21.4 + - - +
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Residues in contact with VAL 43 (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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41A PRO* 3.2 7.2 + - + +
42A ARG* 1.3 73.7 - - - +
44A ASP* 1.3 62.0 + - + +
46A LEU* 3.6 6.2 - - + +
47A LYS* 2.8 30.8 + - - +
132A TYR* 3.6 14.6 - - + +
135A ALA* 4.2 28.5 - - + +
136A LEU* 4.0 27.6 - - + -
139A LEU* 3.6 31.4 - - + -
140A TYR* 5.2 3.1 - - + +
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Residues in contact with ASP 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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42A ARG* 3.6 17.7 - - - +
43A VAL* 1.3 76.3 + - + +
45A ILE* 1.3 83.5 + - - +
47A LYS* 3.7 7.8 - - - +
48A ALA* 3.0 28.6 + - - +
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Residues in contact with ILE 45 (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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29A LEU* 4.0 22.9 - - + -
33A GLU* 4.1 17.5 - - + +
34A VAL* 5.4 1.1 - - - -
42A ARG* 3.3 37.8 + - + +
44A ASP* 1.3 91.5 - - - +
46A LEU* 1.3 67.6 + - - +
48A ALA* 3.3 5.7 + - - +
49A HIS* 3.0 24.1 + - + +
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Residues in contact with LEU 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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29A LEU* 4.7 1.6 - - + -
34A VAL* 4.1 21.1 - - + -
41A PRO* 5.6 0.9 - - + -
42A ARG 3.1 16.2 + - - +
43A VAL* 3.6 6.7 - - + +
45A ILE* 1.3 80.4 - - - +
47A LYS* 1.3 63.1 + - - +
49A HIS* 3.3 3.7 + - - +
50A LEU* 2.9 41.5 + - + +
56A LEU* 3.8 40.2 - - + -
64A ILE* 4.3 4.3 - - + -
131A LEU* 4.3 8.1 - - + +
132A TYR* 4.1 17.0 - - + -
135A ALA* 3.5 31.9 - - + -
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Residues in contact with LYS 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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43A VAL 2.8 21.4 + - - +
44A ASP* 3.7 8.1 - - - +
45A ILE 3.3 0.2 - - - -
46A LEU* 1.3 71.7 - - - +
48A ALA* 1.3 66.3 + - - +
50A LEU* 4.0 2.6 - - - +
51A MET* 2.9 51.7 + - - +
95A PHE* 5.0 2.0 - - - -
99A MET* 3.7 35.7 + - - +
102A PHE* 6.3 0.6 - - - +
103A GLU* 5.2 10.7 + - - +
132A TYR* 3.8 25.3 - - + +
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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
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44A ASP 3.0 17.8 + - - +
45A ILE* 3.3 5.8 + - - +
47A LYS* 1.3 79.0 - - - +
49A HIS* 1.3 64.1 + - - +
51A MET* 3.5 6.9 + - - +
52A LYS* 3.4 36.8 + - - +
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Residues in contact with HIS 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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25A PRO* 3.6 26.2 - - + +
27A HIS* 3.3 23.4 + + - -
29A LEU* 3.4 39.8 - - + +
45A ILE* 3.0 17.0 + - + +
46A LEU* 3.8 2.9 - - - +
48A ALA* 1.3 75.3 - - - +
50A LEU* 1.3 60.0 + - + +
52A LYS* 3.0 27.1 + - - +
54A GLY 3.0 31.2 + - - -
55A ARG 2.9 36.1 + - - -
56A LEU* 4.4 4.3 - - + -
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Residues in contact with LEU 50 (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 LEU* 2.9 39.0 + - + +
49A HIS* 1.3 74.7 - - + +
51A MET* 1.3 61.2 + - - +
53A GLU* 2.9 21.0 + - - -
54A GLY 3.6 20.6 - - - +
56A LEU* 4.4 24.0 - - + -
95A PHE* 3.7 27.7 - - + -
96A PHE* 4.3 4.9 - - - -
128A GLU* 3.9 43.5 - - + +
131A LEU* 4.4 12.3 - - + -
132A TYR* 4.5 5.2 - - + +
170A TYR* 4.9 5.2 - - - +
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Residues in contact with MET 51 (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 LYS* 2.9 50.8 + - + +
48A ALA* 3.8 7.9 - - - +
49A HIS 3.3 0.2 - - - -
50A LEU* 1.3 77.2 - - - +
52A LYS* 1.3 59.4 + - + +
53A GLU* 3.3 1.8 - - - +
95A PHE* 3.9 16.2 - - + -
96A PHE* 3.2 38.3 - - + -
99A MET* 3.7 18.4 - - + -
340A PRO* 5.4 1.0 - - - +
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Residues in contact with LYS 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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22A PRO* 6.5 1.1 - - + -
23A PHE 5.7 2.2 - - - +
24A PRO* 3.4 9.4 - - + +
25A PRO* 3.4 31.7 - - + +
48A ALA* 3.4 28.7 + - - +
49A HIS* 3.0 15.3 + - - +
51A MET* 1.3 79.4 - - + +
53A GLU* 1.3 73.7 + - - +
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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