Contacts of the helix formed by residues 9 - 23 (chain 3) in PDB entry 1LMB
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 GLN 9 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83 THR* 1.3 74.4 - - - +
103 GLU* 1.3 62.7 + - - +
123 LEU* 3.2 16.6 + - - +
133 GLU* 3.0 47.1 + - - +
163 ARG* 3.9 18.8 + - - -
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Residues in contact with GLU 10 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83 THR* 3.2 7.4 + - - +
93 GLN* 1.3 77.1 - - - +
113 GLN* 1.4 57.8 + - - +
133 GLU* 3.1 18.9 + - - +
143 ASP* 2.9 42.3 + - - +
173 ARG* 5.1 3.8 + - - +
783 PRO* 5.4 5.0 - - - +
793 SER* 3.8 29.3 + - - +
823 ARG* 4.9 4.7 + - - -
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Residues in contact with GLN 11 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73 LEU* 3.4 28.4 - - + +
83 THR* 3.0 43.9 + - - +
103 GLU* 1.4 74.2 - - - +
123 LEU* 1.3 64.3 + - - +
143 ASP* 3.4 13.8 + - - +
153 ALA* 3.1 21.8 + - - +
563 ALA* 3.4 27.2 - - + +
573 LEU 5.0 4.5 + - - +
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Residues in contact with LEU 12 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63 PRO* 5.8 3.4 - - + -
73 LEU* 3.8 25.6 - - + +
83 THR 2.9 17.7 + - - +
93 GLN* 3.2 20.2 + - - +
113 GLN* 1.3 78.5 - - - +
133 GLU* 1.3 56.1 - - - +
153 ALA* 3.3 4.6 + - - +
163 ARG* 2.9 50.5 + - - +
523 ASN 5.3 0.4 - - - +
533 GLY* 3.5 33.2 - - - +
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Residues in contact with GLU 13 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93 GLN* 3.0 39.4 + - - +
103 GLU* 3.4 21.1 - - - +
123 LEU* 1.3 71.5 - - - +
143 ASP* 1.3 57.2 + - - +
163 ARG* 3.0 29.8 + - - +
173 ARG* 2.8 58.2 + - - +
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Residues in contact with ASP 14 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103 GLU* 2.9 22.0 + - - +
113 GLN* 3.5 16.7 - - - +
133 GLU* 1.3 77.1 - - - +
153 ALA* 1.4 55.8 + - - +
173 ARG* 2.8 30.1 + - - +
183 LEU* 2.9 30.0 + - - +
573 LEU* 4.5 11.4 - - + +
763 PHE* 3.3 15.5 - - - +
773 SER* 2.8 35.1 + - - -
783 PRO* 4.3 1.7 - - - +
793 SER* 3.6 11.1 + - - -
803 ILE* 4.7 5.2 - - - +
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Residues in contact with ALA 15 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73 LEU* 5.9 0.9 - - + -
113 GLN 3.1 13.1 + - - +
123 LEU 3.6 7.4 - - - +
133 GLU 3.2 0.2 - - - -
143 ASP* 1.4 74.8 - - - +
163 ARG* 1.3 62.7 + - + +
183 LEU* 3.5 7.9 + - - +
193 LYS* 3.0 19.8 + - - +
503 LEU 3.6 23.1 - - - +
513 PHE 3.4 12.1 - - - +
523 ASN 4.6 0.2 - - - -
533 GLY* 3.6 24.9 - - - +
573 LEU* 5.1 4.8 - - + +
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Residues in contact with ARG 16 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93 GLN* 3.9 16.2 + - - -
123 LEU* 2.9 42.0 + - + +
133 GLU* 3.0 40.2 + - - +
153 ALA* 1.3 78.5 - - + +
173 ARG* 1.4 61.1 + - + +
193 LYS* 4.1 3.3 - - - +
203 ALA* 3.1 24.4 + - - +
513 PHE 5.3 0.4 - - - -
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Residues in contact with ARG 17 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103 GLU* 4.6 5.1 + - - +
133 GLU* 2.8 33.7 + - - +
143 ASP* 2.8 38.3 + - - +
163 ARG* 1.4 75.1 - - + +
183 LEU* 1.3 62.2 + - - +
203 ALA* 3.3 7.1 + - - +
213 ILE* 3.1 27.4 + - + +
753 GLU 3.9 15.5 - - - +
763 PHE* 2.8 29.2 + - - -
783 PRO* 4.1 15.9 - - - +
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Residues in contact with LEU 18 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143 ASP 2.9 17.0 + - - +
153 ALA* 3.7 4.0 - - - +
163 ARG 3.4 0.2 - - - -
173 ARG* 1.3 75.6 - - - +
193 LYS* 1.3 62.6 + - - +
213 ILE* 3.2 7.7 + - - +
223 TYR* 3.1 18.9 + - - +
503 LEU 4.6 9.0 - - - +
513 PHE* 3.7 28.7 - - + -
573 LEU* 3.9 21.1 - - + -
653 LEU* 3.8 23.8 - - + -
693 LEU* 3.6 25.8 - - + -
763 PHE* 3.5 35.2 - - + +
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Residues in contact with LYS 19 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31 T 6.1 0.2 - - - -
41 A 2.9 28.8 + - - -
153 ALA 3.0 11.8 + - - +
163 ARG* 4.2 3.8 - - - +
183 LEU* 1.3 77.6 - - - +
203 ALA* 1.3 53.0 + - - +
223 TYR* 3.3 7.3 + - + +
233 GLU* 2.8 57.2 + - + +
333 GLN* 4.9 4.0 - - - +
513 PHE* 3.6 36.1 - - + +
523 ASN* 2.6 31.1 + - - +
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Residues in contact with ALA 20 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163 ARG 3.1 18.4 + - - +
173 ARG* 3.5 7.9 - - - +
183 LEU 3.2 0.2 - - - -
193 LYS* 1.3 76.0 - - - +
213 ILE* 1.3 64.6 + - + +
233 GLU* 3.3 7.4 + - - +
243 LYS* 3.0 25.3 + - - +
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Residues in contact with ILE 21 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173 ARG* 3.1 19.3 + - + +
183 LEU* 3.5 6.7 - - - +
193 LYS 3.2 0.2 - - - -
203 ALA* 1.3 74.7 - - + +
223 TYR* 1.3 66.3 + - - +
243 LYS* 3.1 14.7 + - - +
253 LYS* 2.9 43.8 + - + +
693 LEU* 4.2 16.6 - - + -
713 VAL* 4.0 18.6 - - + -
753 GLU* 4.0 32.8 - - + +
763 PHE* 4.1 22.0 - - + -
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Residues in contact with TYR 22 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31 T 2.7 29.5 + - - -
183 LEU 3.1 12.6 + - - +
193 LYS* 3.5 9.2 - - + +
213 ILE* 1.3 76.1 - - - +
233 GLU* 1.3 80.1 + - - +
253 LYS 4.6 0.2 - - - +
263 LYS* 2.9 52.7 + - + +
313 LEU* 4.1 12.1 - - + -
323 SER* 3.1 19.4 - - - -
333 GLN* 3.0 26.8 + - + -
363 VAL* 4.0 14.6 - - + -
513 PHE* 3.6 41.7 - + + -
693 LEU* 3.9 21.5 - - + +
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Residues in contact with GLU 23 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31 T 4.9 6.1 + - - +
41 A 5.6 0.2 + - - -
193 LYS* 2.8 46.5 + - + +
203 ALA* 3.9 7.0 - - - +
213 ILE 3.2 0.4 - - - -
223 TYR* 1.3 95.6 - - - +
243 LYS* 1.3 62.0 + - - +
263 LYS* 3.7 30.7 + - - +
333 GLN* 5.3 1.7 + - - -
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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
------------------------------------------------------------
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