Contacts of the helix formed by residues 54 - 64 (chain A) in PDB entry 1L0N
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 54 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A GLU* 2.8 10.1 + - - -
52A ASN 3.8 0.2 - - - -
53A ASN* 1.3 75.8 - - - +
55A ALA* 1.3 57.3 + - - +
56A GLY 3.4 2.5 - - - -
57A TYR* 3.3 5.0 + - - +
58A PHE* 2.9 31.4 + - - +
134A ILE* 5.6 0.3 - - - +
167A VAL 3.8 10.1 - - - -
168A GLU 3.4 24.3 - - - +
173A ASN* 5.5 0.2 - - - -
174A VAL* 5.8 1.3 - - - -
177A LEU* 3.9 8.9 - - - +
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Residues in contact with ALA 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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48A GLU* 3.8 5.3 + - - +
52A ASN* 3.0 34.5 + - - +
54A GLY* 1.3 77.4 - - - +
56A GLY* 1.3 58.3 + - - +
58A PHE* 3.3 4.3 + - - +
59A VAL* 3.0 29.1 + - - +
177A LEU* 4.3 3.1 - - + -
181A ASP 5.5 0.7 - - - +
182A LEU* 3.6 17.1 - - + +
185A TYR* 3.7 26.7 - - + -
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Residues in contact with GLY 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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44A GLY 5.1 1.8 + - - -
48A GLU* 4.1 4.2 + - - -
54A GLY 3.4 0.4 - - - -
55A ALA* 1.3 74.9 - - - +
57A TYR* 1.3 55.6 + - - +
58A PHE 3.0 1.6 - - - -
59A VAL* 2.9 6.0 + - - +
60A GLU* 2.8 35.4 + - - +
90A SER* 5.1 5.8 - - - -
95A THR* 5.8 6.9 - - - +
97A TYR* 5.2 0.7 + - - -
185A TYR* 3.7 30.2 + - - -
190A TYR* 5.5 2.3 + - - -
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Residues in contact with TYR 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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54A GLY 3.3 8.8 + - - +
56A GLY* 1.3 75.0 - - - +
58A PHE* 1.3 61.2 + - - +
60A GLU* 3.4 10.8 + - - +
61A HIS* 3.2 43.2 + - - -
90A SER* 4.5 11.4 + - - -
134A ILE* 3.9 23.6 - - + -
137A GLU* 2.6 30.7 + - + +
138A LEU* 5.3 0.7 - - + -
141A ASN* 4.8 3.5 + - - -
167A VAL* 3.7 33.4 + - + +
168A GLU* 3.5 41.8 - - + +
287B ARG* 3.5 20.2 + - - -
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Residues in contact with PHE 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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54A GLY 2.9 15.3 + - - +
55A ALA 3.4 6.3 - - - +
57A TYR* 1.3 76.0 - - - +
59A VAL* 1.3 64.0 + - - +
61A HIS* 3.3 10.9 + - - +
62A LEU* 3.3 17.7 + - + +
127A ILE* 3.4 46.7 - - + -
130A GLU* 4.1 9.4 - - + -
131A ARG* 4.0 23.1 - - + -
134A ILE* 3.7 22.4 - - + -
174A VAL* 3.5 28.5 - - + -
177A LEU* 3.8 21.8 - - + -
182A LEU* 3.7 22.2 - - + -
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Residues in contact with VAL 59 (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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55A ALA 3.0 18.1 + - - +
56A GLY* 2.9 9.8 + - - +
58A PHE* 1.3 74.4 - - - +
60A GLU* 1.3 56.9 + - - +
62A LEU* 2.9 8.8 + - - +
63A ALA* 2.7 39.2 + - + +
97A TYR* 3.7 16.8 - - - +
120A CYS* 5.3 3.1 - - - -
122A LEU* 4.8 8.3 - - + -
182A LEU* 4.5 18.4 - - + -
185A TYR* 4.6 7.2 - - + -
186A LEU* 3.8 41.5 - - + -
190A TYR* 4.0 4.5 - - + +
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Residues in contact with GLU 60 (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 GLY 2.8 15.3 + - - +
57A TYR* 3.5 17.8 - - - +
59A VAL* 1.3 73.2 - - - +
61A HIS* 1.3 65.9 + - - +
63A ALA* 3.3 13.0 + - - +
64A PHE* 4.4 8.3 + - + -
88A ALA* 4.3 21.5 - - + -
89A TYR* 3.7 13.4 - - - +
90A SER* 2.8 28.1 + - - +
95A THR* 6.0 2.7 - - + -
97A TYR* 4.2 14.3 + - + +
286B LYS* 3.5 16.2 + - + -
287B ARG* 2.2 40.6 + - - +
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Residues in contact with HIS 61 (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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57A TYR* 3.2 27.6 + + - -
58A PHE 3.3 10.4 + - - +
59A VAL 3.1 0.2 - - - -
60A GLU* 1.3 82.0 - - - +
62A LEU* 1.3 59.5 + - - +
63A ALA 3.5 0.3 + - - -
64A PHE* 4.2 2.4 + - - +
65A LYS* 3.3 16.6 - - - +
130A GLU* 3.0 43.3 + - + +
133A VAL* 3.7 7.7 - - + +
134A ILE* 3.4 29.3 - - + +
137A GLU* 3.0 43.2 + - - -
287B ARG* 3.3 34.2 - - - +
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Residues in contact with LEU 62 (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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58A PHE* 3.3 29.6 + - + +
59A VAL* 2.9 9.0 + - - +
61A HIS* 1.3 72.3 - - - +
63A ALA* 1.3 66.0 + - - +
64A PHE 3.3 0.4 - - - -
65A LYS* 3.0 22.0 + - + +
66A GLY 4.3 2.1 + - - +
120A CYS* 4.3 8.1 - - - -
121A SER 5.6 2.7 - - - +
122A LEU* 3.6 37.9 - - + -
126A GLN* 3.8 23.6 - - + +
127A ILE* 3.7 41.5 - - + +
130A GLU* 4.0 6.7 - - + -
182A LEU* 3.9 8.3 - - + -
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Residues in contact with ALA 63 (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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59A VAL* 2.7 22.2 + - + +
60A GLU 3.3 10.6 + - - +
62A LEU* 1.3 72.7 - - - +
64A PHE* 1.3 64.8 + - + +
65A LYS 3.7 0.5 + - - -
66A GLY 4.7 4.7 + - - +
67A THR* 5.2 2.4 - - - +
75A LEU* 4.6 1.0 - - - +
97A TYR* 3.5 31.4 - - + +
116A ILE* 3.2 29.9 - - + +
120A CYS* 4.5 12.8 - - - +
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Residues in contact with PHE 64 (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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60A GLU* 4.4 8.0 + - + -
61A HIS 4.2 3.5 + - - +
62A LEU 3.3 0.8 - - - -
63A ALA* 1.3 82.6 - - + +
65A LYS* 1.3 64.3 - - + +
66A GLY 3.4 3.3 + - - -
72A GLY 4.8 1.4 - - - +
75A LEU* 3.8 16.9 - - + +
76A GLU* 3.9 20.1 - - - +
86A LEU* 3.5 52.7 - - + -
87A ASN* 3.6 11.9 - - - -
88A ALA* 3.6 31.9 - - + -
97A TYR* 3.7 21.3 - + + -
116A ILE* 3.9 15.3 - - + -
285B VAL* 3.9 17.7 - - + -
286B LYS* 3.9 17.0 - - + +
287B ARG 6.0 0.4 - - - +
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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