Contacts of the helix formed by residues 53 - 65 (chain A) in PDB entry 2L1R
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 THR 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A ASN 5.6 0.4 - - - +
52A PRO* 1.3 76.1 - - - +
54A PRO* 1.3 76.5 - - + +
55A GLU* 3.3 23.9 + - - +
56A GLU* 3.2 18.2 + - - +
57A LEU* 3.0 17.6 - - - +
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Residues in contact with PRO 54 (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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38A THR* 3.4 22.3 - - - +
39A LYS* 6.4 0.4 - - - -
53A THR* 1.3 84.9 - - + +
55A GLU* 1.3 74.9 + - + +
57A LEU* 3.3 9.5 + - + -
58A GLN* 2.9 27.3 + - - +
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Residues in contact with GLU 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 THR* 3.3 18.0 + - - +
54A PRO* 1.3 101.6 - - + +
56A GLU* 1.3 63.7 + - - +
58A GLN* 3.0 31.5 + - + +
59A GLU* 3.1 15.3 + - - +
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Residues in contact with GLU 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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45A MET* 5.9 0.4 - - - -
52A PRO* 3.5 26.1 - - + +
53A THR* 3.2 19.4 + - - +
55A GLU* 1.3 81.8 - - - +
57A LEU* 1.3 64.7 + - + +
59A GLU* 3.5 16.1 + - - +
60A MET* 3.2 28.6 + - + +
144B ARG* 2.8 35.3 + - - -
146B VAL* 3.5 24.0 - - + +
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Residues in contact with LEU 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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38A THR* 3.8 28.7 - - + +
41A LEU* 3.4 36.3 - - + +
42A GLY* 4.4 9.4 - - - +
45A MET* 3.7 13.7 - - + -
52A PRO* 4.2 12.1 - - + +
53A THR 3.0 24.5 - - - +
54A PRO* 4.1 4.9 - - + -
55A GLU 3.2 0.2 - - - -
56A GLU* 1.3 80.8 - - + +
58A GLN* 1.3 67.4 + - - +
59A GLU 3.1 1.8 - - - -
60A MET* 2.9 39.5 + - + +
61A ILE* 2.9 15.8 + - + +
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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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38A THR* 3.4 15.7 - - + +
54A PRO 2.9 15.7 + - - +
55A GLU* 3.0 21.3 + - + +
57A LEU* 1.3 76.4 - - - +
59A GLU* 1.3 91.0 + - - +
61A ILE* 3.1 6.6 - - + +
62A ASP* 3.0 43.7 + - - +
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Residues in contact with GLU 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 GLU* 3.1 19.4 + - - +
56A GLU* 3.6 12.5 - - - +
57A LEU 3.1 0.2 - - - -
58A GLN* 1.3 109.1 + - - +
60A MET* 1.3 61.9 + - - +
62A ASP* 3.3 7.6 + - + +
63A GLU* 3.0 23.4 + - - +
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Residues in contact with MET 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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41A LEU* 3.7 2.0 - - + -
45A MET* 4.0 5.2 - - + -
56A GLU* 3.2 35.4 + - + +
57A LEU* 2.9 36.2 + - + +
59A GLU* 1.3 80.6 - - + +
61A ILE* 1.3 61.8 + - - +
63A GLU* 3.3 15.2 + - - +
64A VAL* 3.3 19.9 + - - +
72A VAL* 5.7 0.4 - - - -
80A MET* 4.7 2.0 - - - +
91A SXK 3.1 59.5 - - + -
146B VAL* 4.3 17.9 - - + -
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Residues in contact with ILE 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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36A ILE* 3.2 27.6 - - + +
37A SER* 3.7 18.8 - - - +
38A THR* 4.1 5.8 - - + +
41A LEU* 6.2 3.8 - - + -
57A LEU 2.9 11.7 + - - +
58A GLN* 3.1 19.5 - - + +
60A MET* 1.3 77.1 - - - +
62A ASP* 1.3 66.8 + - - +
64A VAL* 3.9 5.4 - - - -
65A ASP* 2.7 39.8 + - - +
70A GLY* 3.3 35.4 - - - +
71A THR* 3.6 2.7 - - - -
72A VAL* 3.6 23.8 - - + +
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Residues in contact with ASP 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 GLN* 3.0 39.1 + - - +
59A GLU* 3.5 9.7 - - + +
61A ILE* 1.3 92.0 - - - +
63A GLU* 1.3 62.3 + - - +
65A ASP 3.0 18.4 + - - +
66A GLU* 3.2 29.1 - - - +
70A GLY* 5.2 3.6 - - - -
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Residues in contact with GLU 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 GLU 3.0 12.8 + - - +
60A MET* 3.6 12.7 - - - +
61A ILE 3.3 0.2 - - - -
62A ASP* 1.3 78.7 - - - +
64A VAL* 1.3 74.3 + - - +
83A ARG* 2.9 35.5 + - - -
91A SXK 4.1 15.4 - - - +
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Residues in contact with VAL 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 MET 3.3 17.3 - - - +
61A ILE 3.5 4.9 - - - +
63A GLU* 1.3 96.2 - - - +
65A ASP* 1.3 63.3 + - + +
72A VAL* 3.7 28.0 - - + -
76A GLU* 3.7 21.0 - - + +
79A VAL* 5.5 8.3 - - + +
80A MET* 3.4 41.1 - - + +
83A ARG* 5.0 5.6 - - - +
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Residues in contact with ASP 65 (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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61A ILE 2.7 24.2 + - - +
62A ASP* 3.0 19.1 - - - +
63A GLU 3.6 0.2 - - - -
64A VAL* 1.3 79.3 - - + +
66A GLU* 1.3 72.6 + - - +
67A ASP* 2.8 12.1 + - - +
70A GLY* 3.0 15.8 + - - -
71A THR 2.9 27.0 + - - +
76A GLU* 3.0 22.0 - - + +
90A CA 2.6 30.2 - - - -
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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