Contacts of the helix formed by residues 50 - 59 (chain P) in PDB entry 1L0V
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 SER 50 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56O TRP* 4.5 0.9 - - - +
44P PHE* 5.6 0.7 - - - -
47P ASP* 3.1 33.4 + - - +
48P ALA 3.4 1.0 - - - -
49P LEU* 1.3 79.1 - - - +
51P TYR* 1.3 66.5 + - - +
52P GLU* 3.8 6.3 + - - +
53P ARG* 2.9 14.4 + - - +
54P VAL* 2.8 22.9 + - - +
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Residues in contact with TYR 51 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49O LEU* 3.5 23.9 + - + -
50O LYS 4.6 1.4 + - - -
52O GLY* 3.1 24.7 + - - -
53O PRO* 3.2 46.7 - - + +
56O TRP* 3.5 43.7 - + + +
50P SER* 1.3 73.9 - - - +
52P GLU* 1.3 71.5 + - + +
54P VAL* 3.0 2.0 + - - +
55P LEU* 2.7 65.1 + - + +
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Residues in contact with GLU 52 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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812O CE1 5.0 16.1 - - - +
50P SER* 3.4 5.8 + - - +
51P TYR* 1.3 95.0 - - + +
53P ARG* 1.3 56.8 + - - +
55P LEU* 4.3 4.4 - - + +
56P ALA* 2.9 29.2 + - - +
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Residues in contact with ARG 53 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126O VAL 3.7 1.6 + - - -
127O ALA 3.8 3.4 + - - -
130O TRP* 2.4 41.8 + - - -
47P ASP* 3.8 18.2 - - - -
48P ALA* 3.1 33.3 + - - +
50P SER* 2.9 19.1 + - - +
52P GLU* 1.3 78.3 - - - +
54P VAL* 1.3 64.0 + - - +
56P ALA* 3.3 5.1 + - - +
57P PHE* 3.1 24.1 + - - +
800P MQ7 2.3 60.1 - - + +
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Residues in contact with VAL 54 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49O LEU* 3.4 28.3 - - + -
56O TRP* 3.7 21.8 - - + -
39P LEU* 5.8 1.3 - - + -
48P ALA 5.0 0.2 - - - +
49P LEU* 4.0 17.5 - - + -
50P SER 2.8 20.0 + - - +
51P TYR 3.5 5.2 - - - +
53P ARG* 1.3 72.3 - - - +
55P LEU* 1.3 56.3 - - - +
57P PHE* 3.2 4.6 + - - +
58P ALA* 2.8 33.4 + - + +
800P MQ7 3.2 46.0 - - + +
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Residues in contact with LEU 55 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49O LEU* 3.5 40.6 - - + +
50O LYS* 5.2 0.4 - - - -
51P TYR* 2.7 53.7 + - + +
52P GLU* 4.3 3.4 - - + +
54P VAL* 1.3 74.5 - - - +
56P ALA* 1.3 53.7 + - - +
57P PHE 3.0 0.2 + - - -
58P ALA 3.1 0.5 + - - -
59P GLN* 2.7 73.3 + - + +
118P ILE* 4.4 13.5 - - + -
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Residues in contact with ALA 56 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52P GLU 2.9 23.8 + - - +
53P ARG* 3.6 7.6 - - - +
54P VAL 3.3 0.2 - - - -
55P LEU* 1.3 75.8 - - - +
57P PHE* 1.3 58.4 + - - +
59P GLN* 3.7 13.0 + - - +
60P SER* 3.4 14.7 + - - -
800P MQ7 3.5 26.1 - - + +
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Residues in contact with PHE 57 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126O VAL* 6.0 3.6 - - + -
53P ARG 3.1 5.1 + - - +
54P VAL 3.4 6.1 - - - +
55P LEU 3.0 0.6 - - - -
56P ALA* 1.3 73.8 - - - +
58P ALA* 1.3 61.4 + - + +
59P GLN 2.9 1.3 - - - -
60P SER* 2.4 38.4 + - - +
62P ILE* 4.7 10.3 - - + -
63P GLY* 3.5 30.4 - - - -
66P PHE* 3.9 22.0 - + + -
67P LEU* 4.9 4.9 - - + -
800P MQ7 3.2 109.0 - + + +
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Residues in contact with ALA 58 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46O LEU* 4.9 1.6 - - + -
49O LEU* 3.5 24.5 - - + -
54P VAL* 2.8 20.7 + - + +
55P LEU* 3.7 3.1 - - - +
57P PHE* 1.3 76.2 - - + +
59P GLN* 1.3 56.9 + - - +
60P SER 3.8 0.2 - - - +
63P GLY 4.7 1.8 - - - -
64P ARG* 3.1 29.1 + - - +
67P LEU* 3.9 27.4 - - + +
115P VAL* 5.3 1.0 - - - +
118P ILE* 4.2 15.5 - - + +
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Residues in contact with GLN 59 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55P LEU* 2.7 60.2 + - + +
56P ALA* 3.9 10.7 - - - +
58P ALA* 1.3 75.9 - - - +
60P SER* 1.3 62.0 + - - +
61P PHE 3.8 0.7 + - - -
64P ARG* 2.8 24.6 + - - +
118P ILE* 3.0 47.6 + - + +
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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