Contacts of the helix formed by residues 50 - 67 (chain B) in PDB entry 2LFH
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A GLU* 5.3 0.9 - - - +
21A GLU* 3.1 43.1 + - - +
22A PRO 5.4 0.7 - - - -
23A LEU* 3.9 19.1 - - - -
49B LEU* 1.3 76.0 - - - +
51B GLN* 1.3 63.7 - - - +
52B VAL* 3.2 12.9 + - - +
53B GLU* 3.1 19.7 + - - +
54B ILE* 3.2 22.9 + - - +
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Residues in contact with GLN 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 3.4 34.5 - - + +
29A MET* 3.8 13.6 - - + +
24B SER* 5.5 1.2 + - - -
29B MET* 4.2 21.6 - - - +
30B ASN* 3.8 25.0 + - - +
33B TYR* 3.2 61.0 + - + +
50B SER* 1.3 73.6 - - - +
52B VAL* 1.3 59.9 + - - +
54B ILE* 3.9 5.8 - - + +
55B LEU* 3.4 8.5 + - - +
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Residues in contact with VAL 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 4.4 7.2 - - + -
24A SER* 3.6 32.3 - - - +
28A ASP* 3.6 20.6 - - + +
29A MET* 3.6 47.8 - - + +
50B SER* 3.1 8.9 - - - +
51B GLN* 1.3 75.8 - - - +
53B GLU* 1.4 64.0 + - - +
54B ILE 3.2 0.2 - - - -
55B LEU* 3.1 24.7 + - - +
56B GLN* 3.3 20.4 + - + +
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Residues in contact with GLU 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLU* 4.0 14.5 - - - +
47B THR* 5.7 0.5 + - - -
48B GLN 3.4 12.4 - - - +
49B LEU* 3.4 12.6 - - + +
50B SER* 3.1 20.7 + - - +
52B VAL* 1.4 73.2 - - - +
54B ILE* 1.3 63.8 + - - +
56B GLN* 3.5 21.0 + - + +
57B ARG* 2.9 61.2 + - - +
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Residues in contact with ILE 54 (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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33B TYR* 3.5 47.8 - - + +
36B LEU* 3.9 24.2 - - + -
37B ARG* 3.3 47.1 - - + +
49B LEU* 4.1 12.5 - - + +
50B SER 3.2 17.4 + - - +
51B GLN* 3.9 6.5 - - + +
53B GLU* 1.3 75.1 - - - +
55B LEU* 1.4 55.7 + - - +
57B ARG* 3.3 5.5 + - - +
58B VAL* 2.9 36.6 + - + +
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Residues in contact with LEU 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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29A MET* 3.9 28.9 - - + +
32A CYS* 3.6 14.1 - - + -
33A TYR* 3.6 35.4 - - + -
36A LEU* 3.8 13.8 - - + +
55A LEU* 3.5 32.1 - - + -
33B TYR* 3.7 9.6 - - + +
36B LEU* 4.9 3.1 - - + -
51B GLN 3.4 17.5 - - - +
52B VAL 3.1 7.1 + - - +
54B ILE* 1.4 76.3 - - - +
56B GLN* 1.3 57.7 + - - +
58B VAL* 3.3 8.2 + - + +
59B ILE* 3.0 34.5 + - - +
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Residues in contact with GLN 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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28A ASP* 3.5 32.5 + - - +
32A CYS* 3.3 23.1 - - - -
35A ARG* 5.8 2.4 + - - +
52B VAL* 3.3 16.6 + - - +
53B GLU* 3.6 25.9 - - + +
55B LEU* 1.3 74.3 - - - +
57B ARG* 1.4 58.4 + - - +
59B ILE* 3.3 10.6 + - - +
60B ASP* 3.0 34.4 + - - +
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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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5A HIS* 5.8 3.4 + - - -
7A HIS* 5.9 7.1 + - - -
40B VAL* 3.9 18.1 - - + +
42B GLY* 4.4 15.2 + - - -
43B VAL* 3.9 24.5 - - + +
44B PRO* 6.0 2.6 - - - +
47B THR* 5.4 2.0 - - - +
49B LEU* 3.2 20.6 - - - +
53B GLU* 2.9 55.6 + - - +
54B ILE* 3.9 4.7 - - - +
56B GLN* 1.4 74.2 - - - +
58B VAL* 1.3 60.0 + - - +
60B ASP* 3.5 14.9 + - + +
61B TYR* 3.0 26.9 + - - +
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Residues in contact with VAL 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU* 4.5 6.5 - - + -
58A VAL* 4.1 12.1 - - + -
62A ILE* 4.0 19.7 - - + -
36B LEU* 3.9 33.9 - - + -
40B VAL* 4.1 16.2 - - + -
54B ILE* 2.9 26.1 + - + +
55B LEU* 3.6 6.7 - - - +
57B ARG* 1.3 74.4 - - + +
59B ILE* 1.4 60.1 + - - +
61B TYR* 3.3 9.1 - - + +
62B ILE* 3.0 49.0 + - + +
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Residues in contact with ILE 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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32A CYS* 3.8 39.0 - - + +
35A ARG* 3.5 59.5 - - + +
36A LEU* 3.7 16.6 - - + -
39A LEU* 4.5 7.4 - - + -
55B LEU 3.0 20.8 + - - +
56B GLN* 3.4 8.5 - - - +
58B VAL* 1.4 75.3 - - - +
60B ASP* 1.4 51.2 + - - +
62B ILE* 3.0 12.3 + - - +
63B LEU* 2.8 47.9 + - + +
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Residues in contact with ASP 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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5A HIS* 5.8 5.0 - - - -
35A ARG* 5.8 1.2 + - - -
56B GLN* 3.0 24.6 + - - +
57B ARG* 3.5 20.9 + - + +
59B ILE* 1.4 74.4 - - - +
61B TYR* 1.3 61.6 + - - +
63B LEU* 3.3 21.5 + - - +
64B ASP* 3.3 20.3 + - - +
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Residues in contact with TYR 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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62A ILE* 3.8 27.0 - - + +
66A GLN* 2.8 39.5 + - - -
39B LEU* 3.2 22.0 + - + -
40B VAL* 4.4 13.0 - - + -
41B PRO* 3.7 25.5 - - + +
57B ARG 3.0 14.8 + - - +
58B VAL* 3.3 14.4 - - + +
59B ILE 3.2 0.2 - - - -
60B ASP* 1.3 77.2 - - - +
62B ILE* 1.3 67.5 + - + +
64B ASP* 3.3 22.3 + - + +
65B LEU* 3.4 36.3 - - + +
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Residues in contact with ILE 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 LEU* 4.4 15.3 - - + -
39A LEU* 3.8 24.2 - - + -
40A VAL* 5.9 0.7 - - + -
58A VAL* 4.4 4.7 - - + -
61A TYR* 3.3 46.4 - - + +
62A ILE* 4.7 5.2 - - + -
65A LEU* 5.3 0.7 - - + -
58B VAL* 3.0 32.4 + - + +
59B ILE* 3.0 8.3 + - - +
61B TYR* 1.3 83.1 - - + +
63B LEU* 1.4 58.2 + - - +
65B LEU* 3.2 11.8 + - + +
66B GLN* 2.9 36.0 + - + +
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Residues in contact with LEU 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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35A ARG* 4.3 14.8 - - - +
39A LEU* 5.2 9.6 - - + -
59B ILE* 2.8 41.9 + - + +
60B ASP* 3.5 26.9 - - - +
61B TYR 3.3 0.4 - - - -
62B ILE* 1.4 70.5 - - + +
64B ASP* 1.3 60.2 + - - +
66B GLN* 4.5 2.9 - - + +
67B VAL* 2.9 28.8 + - - +
68B VAL* 3.8 31.6 + - + +
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Residues in contact with ASP 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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8A HIS* 3.9 27.2 + - + -
60B ASP 3.3 10.8 + - - +
61B TYR* 3.4 14.7 - - + +
63B LEU* 1.3 77.6 - - - +
65B LEU* 1.3 71.0 + - - +
67B VAL* 3.4 17.6 - - - +
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Residues in contact with LEU 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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65A LEU* 3.6 42.8 - - + +
66A GLN* 4.9 4.5 - - - +
61B TYR* 3.4 49.6 - - + +
62B ILE* 3.2 10.7 + - + +
64B ASP* 1.3 89.7 - - - +
66B GLN* 1.3 64.5 + - + +
67B VAL* 4.5 3.2 - - - +
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Residues in contact with GLN 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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39A LEU* 4.6 14.8 + - + -
61A TYR* 2.9 27.0 + - - +
65A LEU* 5.3 8.3 - - - +
62B ILE* 2.9 30.4 + - + +
63B LEU* 6.0 0.2 - - + -
65B LEU* 1.3 78.3 + - - +
67B VAL* 1.4 72.2 + - - +
68B VAL* 4.0 19.5 - - + +
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Residues in contact with VAL 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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63B LEU 2.9 16.5 + - - +
64B ASP* 3.4 20.2 - - - +
65B LEU 4.5 3.4 - - - +
66B GLN* 1.4 82.8 - - - +
68B VAL* 1.3 62.1 - - - +
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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