Contacts of the helix formed by residues 52 - 68 (chain A) in PDB entry 2LAG
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 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A GLU 4.5 2.8 + - - -
43A PHE* 4.2 14.4 + - - -
47A PHE* 3.7 19.7 - - - +
48A GLN 5.1 3.1 - - - +
50A ALA 3.1 3.9 - - - -
51A GLU* 1.3 76.8 - - - +
53A ILE* 1.3 61.6 + - + +
54A PRO* 3.4 1.8 - - - -
55A VAL* 3.1 18.6 + - - +
56A LEU* 2.9 51.5 + - + +
155A THR* 6.0 0.4 - - - -
157A LEU* 3.7 31.8 - - + +
158A GLN* 5.1 5.2 - - - +
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Residues in contact with ILE 53 (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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2A ASP 6.2 0.2 - - - +
50A ALA* 2.9 41.5 + - + +
52A THR* 1.3 79.4 - - + +
54A PRO* 1.4 57.8 - - + +
56A LEU* 3.1 11.8 + - + +
57A HIS* 2.9 27.8 + - + +
95A LEU* 3.1 46.0 - - + +
98A CYS* 3.7 28.5 - - + -
99A VAL* 4.0 4.3 - - + -
105A VAL* 3.8 12.1 - - + -
158A GLN* 5.8 2.0 - - - +
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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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50A ALA 3.6 0.2 - - - +
51A GLU 3.4 17.0 - - - +
52A THR 3.5 0.2 - - - -
53A ILE* 1.4 98.3 - - + +
55A VAL* 1.3 65.7 + - + +
57A HIS* 3.5 5.3 + - + -
58A GLU* 3.1 33.8 + - - +
99A VAL* 5.0 5.6 - - + -
105A VAL* 3.4 26.9 - - + +
106A THR* 4.5 16.4 - - + -
112A LYS* 5.0 14.1 - - + -
116A ILE* 4.2 12.0 - - + +
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Residues in contact with VAL 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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42A GLU 4.5 4.3 - - - +
43A PHE* 4.0 27.6 - - + -
47A PHE* 5.1 5.6 - - + -
51A GLU 4.4 5.6 - - - +
52A THR* 3.1 26.9 + - - +
54A PRO* 1.3 76.3 - - + +
56A LEU* 1.3 55.3 + - - +
58A GLU* 3.3 2.6 + - - +
59A MET* 2.7 35.6 + - - +
112A LYS* 4.3 9.6 - - - +
115A SER* 3.6 46.2 - - - +
116A ILE* 4.1 8.2 - - - +
119A VAL* 4.1 4.8 - - + +
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Residues in contact with LEU 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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43A PHE* 3.7 18.2 - - + -
52A THR* 2.9 35.0 + - + +
53A ILE* 3.1 7.2 + - + +
55A VAL* 1.3 75.4 - - - +
57A HIS* 1.3 62.7 + - - +
59A MET* 3.2 8.0 + - - +
60A ILE* 2.9 30.8 + - + +
95A LEU* 3.6 31.0 - - + -
151A PHE* 6.2 2.0 - - + -
154A SER* 3.5 44.4 - - - +
155A THR* 4.2 18.4 - - + -
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Residues in contact with HIS 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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53A ILE* 2.9 16.7 + - + +
54A PRO* 3.6 8.5 - - + +
56A LEU* 1.3 78.8 - - - +
58A GLU* 1.3 92.4 + - - +
61A GLN* 3.3 28.4 + - - +
92A LEU* 3.2 55.4 + - + +
95A LEU* 3.7 12.7 - - + +
96A GLU* 2.7 42.8 + - + +
99A VAL* 5.6 2.7 - - + -
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Residues in contact with GLU 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 PRO* 3.1 23.8 + - - +
55A VAL 4.0 2.2 - - - +
57A HIS* 1.3 108.6 + - - +
59A MET* 1.3 62.7 + - - +
61A GLN* 3.2 30.1 + - + +
62A GLN* 3.4 12.6 + - - +
116A ILE* 3.8 39.1 - - + +
119A VAL* 4.9 1.9 - - - +
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Residues in contact with MET 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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38A PHE* 5.5 0.9 - - + -
43A PHE* 4.4 15.3 - - + -
55A VAL 2.7 18.3 + - - +
56A LEU* 3.4 9.9 - - - +
58A GLU* 1.3 75.3 - - - +
60A ILE* 1.3 64.5 + - - +
62A GLN* 3.1 14.9 + - - +
63A ILE* 3.1 41.9 + - + +
119A VAL* 3.8 29.6 - - + +
122A TYR* 6.0 0.4 - - + -
123A PHE* 4.2 12.3 - - + -
147A ILE 4.9 0.4 - - - +
150A SER* 3.9 27.8 - - - +
151A PHE* 3.9 15.3 - - + +
154A SER* 3.7 27.1 - - - +
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Residues in contact with ILE 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 LEU 2.9 15.2 + - - +
58A GLU 3.4 0.2 - - - -
59A MET* 1.3 74.3 - - - +
61A GLN* 1.3 55.9 + - - +
63A ILE* 3.1 7.3 + - + +
64A PHE* 2.7 34.1 + - + +
88A LEU* 3.8 28.7 - - + +
91A GLN* 3.6 23.6 - - + -
92A LEU* 3.7 31.2 - - + +
95A LEU* 3.6 28.9 - - + -
151A PHE* 3.6 31.4 - - + -
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Residues in contact with GLN 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 HIS* 3.3 25.7 - - - +
58A GLU* 3.2 28.0 - - + +
59A MET 3.1 0.2 - - - -
60A ILE* 1.3 78.6 - - - +
62A GLN* 1.3 60.2 + - + +
64A PHE* 3.5 6.7 + - - +
65A ASN* 3.0 30.4 + - - +
92A LEU* 3.5 32.7 - - - +
96A GLU* 5.5 0.2 + - - -
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Residues in contact with GLN 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 GLU 3.4 11.2 + - - +
59A MET 3.1 9.5 + - - +
61A GLN* 1.3 80.4 - - + +
63A ILE* 1.3 58.8 + - - +
65A ASN* 3.4 15.2 + - - +
66A LEU* 2.8 32.7 + - - +
119A VAL* 4.4 10.8 - - + -
120A ARG* 3.7 49.2 + - + +
123A PHE* 3.6 39.6 - - + +
124A GLN* 4.6 8.9 + - - +
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Residues in contact with ILE 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 MET* 3.1 30.0 + - + +
60A ILE* 3.1 12.7 + - + +
62A GLN* 1.3 75.8 - - - +
64A PHE* 1.3 63.2 + - - +
66A LEU* 3.2 3.1 + - - +
67A PHE* 2.9 50.4 + - + +
84A PHE* 3.9 23.1 - - + -
88A LEU* 4.0 8.3 - - + -
123A PHE* 3.5 22.9 - - + -
147A ILE* 4.1 13.5 - - + -
151A PHE* 3.7 31.4 - - + -
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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 ILE* 2.7 21.9 + - + +
61A GLN* 3.7 8.1 - - - +
63A ILE* 1.3 74.0 - - - +
65A ASN* 1.3 54.7 + - - +
67A PHE* 3.7 1.6 - - - +
68A SER* 2.7 52.2 + - - -
85A TYR* 3.3 51.4 - + + -
88A LEU* 3.7 30.0 - - + +
89A TYR* 3.5 37.0 - + - -
92A LEU* 4.7 9.4 - - + -
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Residues in contact with ASN 65 (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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61A GLN 3.0 19.1 + - - +
62A GLN* 3.7 16.6 + - - +
64A PHE* 1.3 78.1 - - - +
66A LEU* 1.3 63.4 + - - +
68A SER* 3.4 10.5 + - - -
69A THR* 3.3 22.0 + - - +
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Residues in contact with LEU 66 (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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62A GLN 2.8 23.0 + - - +
63A ILE 3.6 3.1 - - - +
65A ASN* 1.3 75.9 - - - +
67A PHE* 1.3 73.0 + - + +
69A THR* 2.6 32.7 + - + +
72A SER* 2.8 10.3 + - - +
123A PHE* 4.2 25.4 - - + +
126A ILE* 4.5 10.1 - - + -
127A THR* 4.9 17.5 - - + +
130A LEU* 4.2 22.4 - - + -
140A TRP* 5.9 1.1 - - + -
143A VAL* 4.3 20.0 - - + -
147A ILE* 4.5 2.7 - - + -
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Residues in contact with PHE 67 (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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18A LEU* 4.1 25.1 - - + -
21A MET* 4.4 3.4 - - + -
63A ILE* 2.9 46.1 + - + +
64A PHE 4.1 1.8 - - - +
66A LEU* 1.3 86.2 - - + +
68A SER* 1.3 58.6 + - - +
69A THR 3.0 10.5 + - - -
72A SER* 3.1 18.7 - - - -
73A SER* 3.5 4.3 + - - -
76A TRP* 3.5 40.8 - + - -
81A LEU* 3.9 9.6 - - + +
84A PHE* 3.7 20.0 - + + -
85A TYR* 2.9 25.3 + - + -
143A VAL* 5.5 3.1 - - + -
144A ARG* 5.0 6.3 - - - -
147A ILE* 4.1 25.1 - - + -
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Residues in contact with SER 68 (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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64A PHE* 2.7 42.5 + - - -
65A ASN* 3.4 7.5 + - - -
67A PHE* 1.3 70.2 - - - +
69A THR* 1.3 63.7 + - - +
70A LYS* 3.9 0.7 + - - +
73A SER* 3.9 4.9 + - - -
85A TYR* 3.4 19.2 - - - -
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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