Contacts of the helix formed by residues 41 - 51 (chain A) in PDB entry 1LU9
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 ASN 41 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A ASN* 3.2 22.6 + - - +
37A VAL* 3.5 8.4 - - - +
38A THR* 2.8 32.0 + - - +
40A ASP* 1.3 75.4 - - - +
42A VAL* 1.3 66.3 + - - +
43A GLY 3.1 3.4 + - - -
44A ALA* 3.6 13.0 + - - +
45A TYR* 3.8 28.6 + - + -
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Residues in contact with VAL 42 (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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9A PHE* 3.7 28.7 - - + -
37A VAL* 3.6 20.2 - - + -
38A THR 3.1 15.2 + - - +
39A PRO* 3.8 11.2 - - + +
41A ASN* 1.3 81.7 + - - +
43A GLY* 1.3 70.3 + - - +
45A TYR* 3.0 9.3 + - + +
46A VAL* 2.9 22.0 + - + +
76A VAL* 4.1 9.2 - - + +
79A ALA* 3.8 23.6 - - + -
80A VAL* 3.8 16.4 - - + -
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Residues in contact with GLY 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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39A PRO 4.5 1.8 + - - -
40A ASP 4.1 6.7 + - - -
41A ASN 3.1 2.0 - - - -
42A VAL* 1.3 84.3 - - - +
44A ALA* 1.3 60.8 + - - +
46A VAL* 3.2 3.8 + - - +
47A ASP* 3.0 18.5 + - - -
79A ALA 5.6 0.4 - - - -
83A ARG* 3.2 45.1 + - - -
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Residues in contact with ALA 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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40A ASP 5.3 0.8 + - - -
41A ASN* 3.6 8.5 + - - +
42A VAL 3.3 0.4 - - - -
43A GLY* 1.3 75.2 - - - +
45A TYR* 1.3 68.0 + - + +
47A ASP* 3.3 15.1 + - - +
48A GLY* 3.3 16.5 + - - -
83A ARG* 3.9 4.7 - - - +
17B VAL* 5.2 0.5 - - - +
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Residues in contact with TYR 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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9A PHE* 3.5 35.7 - + + -
34A TYR* 3.7 18.7 - + - +
35A GLY 5.0 2.6 + - - -
37A VAL* 4.1 16.8 - - + -
41A ASN* 3.8 39.5 + - + +
42A VAL* 3.0 16.2 + - + +
44A ALA* 1.3 82.5 - - + +
46A VAL* 1.3 61.6 + - - +
48A GLY 3.1 10.4 + - - -
49A THR* 3.4 9.0 + - - +
14B THR* 2.7 39.6 + - - +
15B PRO 4.7 3.1 - - - -
16B SER* 6.2 0.7 - - - -
17B VAL* 3.5 31.5 - - + +
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Residues in contact with VAL 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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9A PHE* 4.3 1.1 - - + -
42A VAL* 2.9 22.4 + - + +
43A GLY* 3.6 7.6 - - - +
45A TYR* 1.3 72.5 - - - +
47A ASP* 1.3 65.7 + - - +
49A THR* 2.8 28.5 + - - +
50A ILE* 3.1 11.0 + - + +
63A ILE* 4.1 7.9 - - + -
80A VAL* 3.9 38.1 - - + +
83A ARG* 3.5 26.2 - - + -
84A PHE* 3.8 27.1 - - + -
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Residues in contact with ASP 47 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A GLY 3.0 13.2 + - - +
44A ALA* 3.4 13.2 - - - +
45A TYR 3.2 0.4 - - - -
46A VAL* 1.3 76.1 - - - +
48A GLY* 1.3 62.9 + - - +
50A ILE* 3.1 9.0 + - - +
51A TYR* 3.0 56.5 + - + +
83A ARG* 2.6 44.4 + - - +
18B PHE* 5.4 1.1 - - - -
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Residues in contact with GLY 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 ALA 3.3 5.3 + - - -
45A TYR 3.1 9.3 + - - -
47A ASP* 1.3 81.3 - - - +
49A THR* 1.3 55.0 + - - +
52A THR* 2.8 28.9 + - - +
17B VAL* 3.7 7.9 - - - -
18B PHE* 3.7 33.6 - - - -
21B VAL* 3.9 6.2 - - - +
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Residues in contact with THR 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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7A PHE* 4.0 21.1 - - + -
9A PHE* 4.8 1.1 - - + -
45A TYR 3.6 13.7 - - - +
46A VAL* 2.8 16.4 + - - +
48A GLY* 1.3 78.6 - - - +
50A ILE* 1.3 60.3 + - - +
51A TYR 3.6 0.2 - - - -
52A THR* 4.0 8.4 + - - -
53A ARG* 5.1 5.7 + - - +
58A LYS* 5.9 2.3 - - - +
61A THR* 3.9 21.1 + - + +
63A ILE* 3.7 20.4 - - + +
90A VAL* 3.6 33.3 - - - +
17B VAL* 3.8 12.8 - - + -
21B VAL* 5.0 0.7 - - - -
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Residues in contact with ILE 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 VAL* 3.1 17.4 + - + +
47A ASP* 3.6 13.2 - - - +
49A THR* 1.3 90.1 - - - +
51A TYR* 1.3 95.7 + - + +
52A THR 3.6 1.6 - - - -
53A ARG 4.6 8.2 - - - +
58A LYS* 4.8 6.0 - - - +
83A ARG 4.0 17.3 - - - +
84A PHE* 4.1 9.2 - - + -
85A PHE* 4.7 0.7 - - + -
88A PHE* 3.7 37.0 - - + +
89A ARG* 3.6 35.2 - - - +
90A VAL* 5.0 0.7 - - - -
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Residues in contact with TYR 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 ASP* 3.0 50.9 + - + +
50A ILE* 1.3 100.6 - - + +
52A THR* 1.3 62.1 + - - +
53A ARG 3.7 1.6 - - - -
85A PHE* 2.8 33.2 - + - -
88A PHE* 4.1 26.5 - + - -
18B PHE* 3.7 21.4 - + + -
224B GLN* 6.0 0.2 + - - -
257B LEU* 3.7 14.6 - - - +
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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