Contacts of the helix formed by residues 42 - 52 (chain C) in PDB entry 1LFD
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 ALA 42 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41C LYS* 1.3 70.3 - - - +
43C PRO* 1.4 66.2 - - + +
44C THR 3.1 0.5 + - - -
45C VAL* 3.1 3.0 + - - +
46C ILE* 2.8 44.1 + - + +
65C LEU* 5.2 3.4 - - + -
77C ILE* 4.1 13.9 - - + +
78C PRO 3.4 26.2 - - - +
79C GLU* 3.4 6.7 - - - +
81C ALA 2.8 12.5 + - - +
83C VAL* 3.8 10.2 - - - +
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Residues in contact with PRO 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C LYS* 3.5 14.8 - - + -
42C ALA* 1.4 87.4 - - - +
44C THR* 1.3 59.4 + - - +
46C ILE* 3.9 12.6 - - + +
47C ARG* 3.2 25.5 + - - +
60C PRO* 4.3 15.3 - - + +
61C GLU* 5.2 6.5 - - - +
79C GLU 3.3 20.6 - - - +
80C ASN* 4.3 12.1 - - - +
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Residues in contact with THR 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262B GLU* 5.3 1.1 - - - +
265B SER* 3.4 24.5 - - - +
266B ALA* 4.9 4.9 - - + +
40C ASP* 3.9 19.7 - - - +
41C LYS* 2.9 24.7 + - - +
43C PRO* 1.3 78.5 - - - +
45C VAL* 1.3 62.8 - - - +
46C ILE 3.2 0.2 - - - -
47C ARG* 3.4 6.5 + - - +
48C LYS* 3.2 29.3 + - - +
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Residues in contact with VAL 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C ILE* 4.0 5.2 - - + -
34C ILE* 3.8 19.9 - - + +
36C VAL* 3.9 23.6 - - + -
40C ASP* 3.7 24.5 - - + +
41C LYS 3.8 0.9 - - - +
42C ALA 3.1 6.1 + - - +
44C THR* 1.3 73.8 - - - +
46C ILE* 1.3 60.1 + - - +
48C LYS* 3.3 11.0 + - + +
49C ALA* 2.9 26.7 + - - +
65C LEU* 3.6 23.3 - - + -
83C VAL* 3.5 29.2 - - + -
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Residues in contact with ILE 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C ALA* 2.8 36.8 + - + +
43C PRO* 3.9 8.5 - - + +
45C VAL* 1.3 77.8 - - - +
47C ARG* 1.3 51.4 + - - +
49C ALA* 3.1 7.3 + - - +
50C MET* 2.8 58.1 + - - +
60C PRO* 3.8 20.0 - - + +
63C TYR* 3.7 35.0 - - + +
64C GLU* 4.4 7.4 - - - -
65C LEU* 4.5 18.2 - - + +
79C GLU* 5.6 1.1 - - - +
97C LEU* 4.0 9.2 - - + -
100C ARG* 6.1 0.4 - - - +
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Residues in contact with ARG 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262B GLU* 3.5 23.6 - - - +
43C PRO 3.2 15.9 + - - +
44C THR* 3.6 7.0 - - - +
45C VAL 3.3 0.2 - - - -
46C ILE* 1.3 77.5 - - - +
48C LYS* 1.3 58.1 + - - +
50C MET* 3.3 37.6 - - - +
51C ASP* 3.0 67.9 + - - +
55C LEU 3.4 5.5 + - - -
56C ASP* 3.4 20.3 + - - +
58C ASP 3.6 12.3 + - - -
59C GLU* 4.4 5.5 + - - -
60C PRO* 4.1 19.4 - - + +
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Residues in contact with LYS 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262B GLU* 3.3 43.3 - - + +
263B GLU* 2.8 33.3 + - - +
265B SER* 4.0 10.9 - - - +
266B ALA 5.5 0.4 - - - +
34C ILE* 4.0 13.1 - - + +
35C LEU 2.7 30.1 + - - +
36C VAL* 4.2 0.2 - - - +
37C THR* 4.3 4.2 - - - +
40C ASP* 2.8 25.8 + - - -
44C THR* 3.2 18.7 + - - +
45C VAL* 3.5 13.9 - - + +
46C ILE 3.2 0.2 - - - -
47C ARG* 1.3 77.0 - - - +
49C ALA* 1.3 58.8 + - - +
51C ASP* 3.7 1.7 + - - +
52C LYS* 3.0 30.1 + - - +
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Residues in contact with ALA 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C VAL* 3.9 24.9 - - + -
34C ILE* 4.0 8.9 - - + +
45C VAL 2.9 17.5 + - - +
46C ILE* 3.4 5.8 - - - +
48C LYS* 1.3 77.5 - - - +
50C MET* 1.3 56.2 + - - +
52C LYS* 3.3 5.5 + - - +
53C HIS* 2.9 35.9 + - - +
65C LEU* 5.1 3.4 - - + -
97C LEU* 3.7 22.4 - - + -
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Residues in contact with MET 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C ILE* 2.8 26.3 + - + +
47C ARG* 3.3 23.6 - - - +
48C LYS 3.3 0.2 - - - -
49C ALA* 1.3 70.5 - - - +
51C ASP* 1.3 65.3 + - - +
53C HIS 3.0 2.8 + - - -
54C ASN 2.9 5.4 + - - -
55C LEU* 2.8 55.2 + - + +
58C ASP* 3.3 31.9 - - + +
59C GLU 3.8 2.0 - - - -
60C PRO* 3.7 29.2 - - - -
63C TYR* 3.6 18.2 - - + -
97C LEU* 4.0 16.2 - - + -
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Residues in contact with ASP 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262B GLU* 3.6 28.7 - - + +
47C ARG* 3.0 49.6 + - - +
48C LYS* 4.1 4.3 - - - +
50C MET* 1.3 73.7 - - - +
52C LYS* 1.3 62.0 + - - +
54C ASN 3.2 3.3 + - - -
56C ASP* 3.3 24.6 - - - +
231D LYS* 2.6 31.8 + - - +
233D ASP* 5.1 0.9 - - - -
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Residues in contact with LYS 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263B GLU* 4.7 9.7 + - - +
32C LYS* 2.8 47.4 + - + +
33C SER 3.5 19.4 + - - +
34C ILE* 3.8 18.2 - - + -
48C LYS 3.0 20.3 + - - +
49C ALA* 3.4 6.3 - - - +
51C ASP* 1.3 79.2 - - - +
53C HIS* 1.3 59.0 + - + +
54C ASN* 3.3 3.2 + - - +
233D ASP* 2.9 32.1 + - - +
234D PRO 2.8 30.7 + - - -
235D THR* 4.0 7.6 + - - +
236D ILE* 4.6 2.6 - - - +
238D ASP* 4.3 18.6 - - - -
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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