Contacts of the helix formed by residues 52 - 67 (chain B) in PDB entry 1LT8
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 HIS 52 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A ARG* 3.8 30.3 + - - -
38B TYR* 3.6 39.6 - + + -
48B ALA* 2.7 23.3 + - + +
51B GLU* 1.3 103.0 + - + +
53B PRO* 1.3 66.0 - - - +
54B GLU* 2.8 20.9 + - - +
55B ALA* 3.2 13.5 + - + +
56B VAL* 3.4 6.6 + - - +
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Residues in contact with PRO 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B ALA 3.6 1.5 - - - +
49B ALA 4.1 9.0 - - - +
50B VAL 4.4 7.2 - - - +
51B GLU 3.9 5.8 - - - +
52B HIS* 1.3 84.8 - - - +
54B GLU* 1.3 71.7 + - + +
56B VAL* 3.1 3.9 + - + +
57B ARG* 2.5 54.0 + - - +
102B ALA* 6.2 0.9 - - + -
106B ILE* 3.7 25.3 - - + +
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Residues in contact with GLU 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLN* 4.4 14.8 - - - +
61A ARG* 4.4 21.7 + - - +
38B TYR* 5.4 2.3 + - - -
52B HIS* 2.8 39.5 + - - +
53B PRO* 1.3 84.1 - - + +
55B ALA* 1.3 61.4 + - - +
57B ARG* 3.7 18.5 - - - +
58B GLN* 2.8 31.4 + - - +
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Residues in contact with ALA 55 (chain B).
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* 3.9 13.1 + - - +
62A GLU* 5.5 0.7 - - - +
33B LEU* 4.2 7.8 - - + +
36B ARG* 5.4 1.7 + - - -
38B TYR* 3.6 50.3 - - + -
52B HIS* 3.3 11.7 - - + +
53B PRO 3.1 0.4 - - - -
54B GLU* 1.3 84.2 + - - +
56B VAL* 1.3 62.8 + - + +
58B GLN* 3.8 2.3 - - - +
59B LEU* 3.2 21.8 + - - +
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Residues in contact with VAL 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B PHE* 3.7 12.7 - - + -
33B LEU* 4.5 7.6 - - + -
48B ALA* 3.8 26.5 - - + +
49B ALA* 4.0 4.0 - - + -
52B HIS 3.5 14.6 - - - +
53B PRO 3.1 5.6 + - - +
55B ALA* 1.3 76.6 - - + +
57B ARG* 1.3 63.3 + - - +
59B LEU* 3.4 4.0 + - - +
60B HIS* 3.1 50.3 + - + +
74B PHE* 3.9 29.6 - - + -
103B ALA* 5.8 0.9 - - - -
106B ILE* 4.1 13.9 - - + -
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Residues in contact with ARG 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B PRO* 2.5 32.6 + - - +
54B GLU* 3.7 27.2 - - - +
56B VAL* 1.3 74.7 - - - +
58B GLN* 1.3 56.3 + - - +
60B HIS* 3.2 4.9 + - - +
61B ARG* 2.9 68.3 + - - +
106B ILE* 3.6 32.5 - - + +
109B GLN* 2.7 33.3 + - - +
110B VAL* 4.0 9.2 - - + -
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Residues in contact with GLN 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A TYR* 3.2 30.5 + - - -
54A GLU* 4.1 20.4 - - - +
55A ALA* 3.6 18.8 - - - +
58A GLN* 3.8 28.5 - - + -
36B ARG* 5.0 2.5 - - - +
54B GLU 2.8 22.1 + - - +
55B ALA 3.8 4.0 - - - +
57B ARG* 1.3 72.8 - - - +
59B LEU* 1.3 57.6 + - - +
61B ARG* 3.3 15.3 + - - +
62B GLU* 2.9 61.1 + - - +
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Residues in contact with LEU 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B PHE* 3.4 33.2 - - + -
32B ALA* 3.8 18.2 - - + -
33B LEU* 3.8 22.4 - - + -
36B ARG* 3.6 33.6 - - - +
55B ALA 3.2 11.7 + - - +
56B VAL 3.7 8.3 - - - +
58B GLN* 1.3 75.9 - - - +
60B HIS* 1.3 66.1 + - - +
62B GLU* 3.1 10.9 + - - +
63B PHE* 3.0 57.3 + - + -
304B PRO* 4.5 2.0 - - + -
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Residues in contact with HIS 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B ASP* 4.8 0.2 - - - -
29B PHE* 3.4 30.5 - + - -
56B VAL* 3.1 34.0 + - + +
57B ARG 3.4 7.6 - - - +
59B LEU* 1.3 74.6 - - - +
61B ARG* 1.3 58.8 + - - +
63B PHE* 3.1 6.3 + - - +
64B LEU* 2.8 24.8 + - - +
71B MET* 3.5 36.6 - - + +
72B GLN 3.1 25.2 + - - -
74B PHE* 4.6 6.7 - - + -
103B ALA 5.1 1.3 - - - -
106B ILE* 3.9 8.8 - - + +
107B ALA* 4.0 21.4 - - + +
110B VAL* 3.8 21.3 - - + -
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Residues in contact with ARG 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A TYR* 4.5 5.8 - - - +
54A GLU* 5.2 14.3 - - - +
57B ARG* 2.9 52.5 + - - +
58B GLN* 3.6 20.4 + - - +
60B HIS* 1.3 77.3 - - - +
62B GLU* 1.3 52.8 + - - +
64B LEU* 3.1 4.6 + - + +
65B ARG* 2.7 37.1 + - - +
109B GLN* 4.0 13.3 - - - +
110B VAL* 3.7 12.3 - - + +
113B GLU* 2.7 43.9 + - - +
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Residues in contact with GLU 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ARG* 3.1 40.5 + - - +
38A TYR* 3.5 18.0 - - + +
55A ALA* 5.3 1.7 - - - +
36B ARG* 2.8 38.4 + - - -
58B GLN* 2.9 45.8 + - - +
59B LEU* 3.1 8.7 + - - +
61B ARG* 1.3 75.1 - - - +
63B PHE* 1.3 59.2 + - - +
65B ARG* 3.3 3.6 + - - +
66B ALA* 2.9 28.4 + - - +
304B PRO* 3.5 18.2 - - + +
324B ALA* 5.7 0.2 - - - +
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Residues in contact with PHE 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B ASP* 4.0 7.0 - - + -
27B GLY* 3.3 39.0 - - - -
28B GLY 4.1 2.7 - - - -
29B PHE* 3.5 27.8 - + - -
32B ALA* 5.2 0.9 - - + -
59B LEU* 3.0 52.8 + - + -
60B HIS* 3.5 6.1 - - - +
62B GLU* 1.3 76.0 - - - +
64B LEU* 1.3 61.6 + - - +
66B ALA* 3.0 11.2 + - - +
67B GLY 3.1 1.0 + - - -
68B SER* 3.0 31.8 + - - +
71B MET* 4.5 1.8 - - + -
302B PHE 3.6 10.5 - - - -
303B GLU* 3.6 5.8 - - - -
304B PRO* 3.6 27.6 - - + -
307B ILE* 3.6 15.7 - - + -
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Residues in contact with LEU 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B HIS 2.8 13.3 + - - +
61B ARG* 3.4 9.6 - - + +
63B PHE* 1.3 75.1 - - - +
65B ARG* 1.3 59.2 + - - +
67B GLY* 3.0 19.6 + - - -
68B SER 3.8 10.4 + - - +
71B MET* 3.7 16.1 - - + +
110B VAL* 3.3 32.5 - - + +
113B GLU* 3.9 26.2 - - + +
114B GLY* 3.9 9.6 - - - +
115B ASP 4.9 1.6 - - - +
116B ALA* 3.4 33.2 - - + -
323B PRO* 4.7 4.5 - - - +
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Residues in contact with ARG 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ARG 4.6 3.6 - - - -
37A GLY 2.7 29.6 + - - -
38A TYR* 3.5 28.6 - - - +
52A HIS* 3.5 36.2 + - - -
61B ARG 2.7 20.2 + - - +
62B GLU* 3.6 4.3 - - - +
64B LEU* 1.3 74.3 - - - +
66B ALA* 1.3 58.9 + - - +
67B GLY 3.2 0.2 - - - -
323B PRO* 3.2 47.2 + - + +
324B ALA* 3.0 36.2 + - + +
326B GLU* 5.2 1.6 - - - +
327B LYS* 3.7 23.8 - - - +
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Residues in contact with ALA 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B GLU 2.9 18.7 + - - +
63B PHE* 3.0 7.6 + - - +
65B ARG* 1.3 78.0 - - - +
67B GLY* 1.3 58.0 + - - +
304B PRO* 3.2 31.4 - - + +
307B ILE* 4.0 8.1 - - + -
308B ARG* 3.3 27.7 + - + +
311B ALA* 3.7 3.1 - - - +
322B PRO* 3.4 13.1 - - - +
324B ALA* 4.0 11.9 - - + +
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Residues in contact with GLY 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ILE* 3.6 21.8 - - - +
64B LEU 3.0 10.0 + - - -
65B ARG 3.2 1.2 - - - -
66B ALA* 1.3 79.6 - - - +
68B SER* 1.3 68.3 + - - +
69B ASN* 3.5 10.4 + - - +
311B ALA* 4.5 6.3 - - - -
318B ARG* 4.0 6.8 + - - -
320B PHE* 6.5 0.2 - - - -
322B PRO* 3.8 12.6 - - - -
323B PRO* 5.4 0.9 - - - -
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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