Contacts of the helix formed by residues 9 - 23 (chain 4) 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 4).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84 THR* 1.3 76.8 - - - +
104 GLU* 1.3 63.4 + - - +
124 LEU* 3.2 12.7 + - + +
134 GLU* 3.1 36.3 + - + +
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Residues in contact with GLU 10 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84 THR* 3.0 8.8 + - - +
94 GLN* 1.3 80.0 - - - +
114 GLN* 1.3 70.1 + - + +
134 GLU* 3.3 10.3 + - + +
144 ASP* 3.1 30.7 + - - +
174 ARG* 4.4 2.9 + - - +
794 SER* 3.7 32.9 + - - +
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Residues in contact with GLN 11 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64 PRO 4.7 0.7 - - - +
74 LEU* 3.3 29.1 - - + +
84 THR* 2.8 42.9 + - - +
104 GLU* 1.3 79.6 - - + +
124 LEU* 1.4 57.9 + - - +
144 ASP* 3.4 13.1 - - - +
154 ALA* 3.1 27.0 + - - +
564 ALA* 3.7 25.2 - - + +
574 LEU* 5.1 4.2 + - - +
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Residues in contact with LEU 12 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74 LEU* 4.1 17.5 - - + +
84 THR 3.2 19.2 + - - +
94 GLN* 3.6 12.8 - - + +
104 GLU 3.1 0.8 - - - -
114 GLN* 1.4 75.6 - - - +
134 GLU* 1.3 65.2 + - + +
154 ALA* 3.5 5.1 + - - +
164 ARG* 3.2 21.7 + - - +
524 ASN 5.3 1.3 - - - +
534 GLY* 3.8 31.6 - - - +
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Residues in contact with GLU 13 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94 GLN* 3.1 30.6 + - + +
104 GLU* 3.3 10.2 + - + +
124 LEU* 1.3 78.1 - - + +
144 ASP* 1.4 54.6 + - - +
164 ARG* 3.2 7.7 + - + +
174 ARG* 2.8 66.6 + - - +
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Residues in contact with ASP 14 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104 GLU* 3.1 17.4 + - - +
114 GLN* 3.4 16.9 - - - +
134 GLU* 1.4 78.9 - - - +
154 ALA* 1.3 55.8 + - - +
174 ARG* 2.7 31.2 + - - +
184 LEU* 2.9 29.9 + - - +
574 LEU* 4.4 11.6 - - + +
764 PHE* 3.2 16.0 - - - +
774 SER* 2.8 34.9 + - - -
784 PRO* 4.4 1.0 - - - +
794 SER* 3.8 10.7 + - - -
804 ILE* 4.7 6.2 - - - +
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Residues in contact with ALA 15 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74 LEU* 5.1 1.6 - - + -
114 GLN 3.1 15.7 + - - +
124 LEU 3.8 5.6 - - - +
144 ASP* 1.3 75.3 - - - +
164 ARG* 1.4 59.0 + - - +
184 LEU* 3.4 8.6 + - - +
194 LYS* 3.0 24.3 + - - +
504 LEU 3.5 23.1 - - - +
514 PHE 3.4 12.4 - - - +
534 GLY* 3.8 23.3 - - - +
554 ASN 5.9 0.2 - - - +
574 LEU* 5.1 3.6 - - + +
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Residues in contact with ARG 16 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124 LEU 3.2 12.2 + - - +
134 GLU* 3.2 11.9 + - + +
154 ALA* 1.4 71.9 - - - +
174 ARG* 1.4 67.7 + - + +
194 LYS* 3.5 7.1 + - + +
204 ALA* 3.1 25.6 + - - +
514 PHE 5.2 0.4 - - - -
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Residues in contact with ARG 17 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104 GLU* 4.4 4.4 + - - +
134 GLU* 2.8 41.9 + - - +
144 ASP* 2.7 39.3 + - - +
164 ARG* 1.4 78.0 - - + +
184 LEU* 1.3 62.5 + - - +
204 ALA* 3.2 8.2 + - - +
214 ILE* 3.2 25.3 + - + +
754 GLU 4.1 13.7 - - - +
764 PHE* 2.9 30.9 + - + -
784 PRO* 4.4 12.8 - - - +
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Residues in contact with LEU 18 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144 ASP 2.9 19.8 + - - +
154 ALA* 3.7 4.0 - - - +
174 ARG* 1.3 73.1 - - - +
194 LYS* 1.3 63.1 + - - +
214 ILE* 3.3 6.9 + - + +
224 TYR* 3.1 19.6 + - - +
504 LEU* 4.6 11.7 - - + +
514 PHE* 3.8 29.6 - - + -
574 LEU* 4.0 20.2 - - + -
654 LEU* 3.9 22.4 - - + -
694 LEU* 3.7 26.0 - - + -
764 PHE* 3.7 34.4 - - + +
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Residues in contact with LYS 19 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242 A 2.6 34.9 + - - -
154 ALA 3.0 18.7 + - - +
164 ARG* 3.9 7.4 - - + +
184 LEU* 1.3 76.7 - - - +
204 ALA* 1.3 58.0 + - - +
224 TYR* 3.4 8.2 + - + +
234 GLU* 2.9 52.6 + - + +
334 GLN* 5.6 0.2 - - - +
514 PHE* 3.8 38.3 + - + +
524 ASN* 2.8 21.0 + - - +
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Residues in contact with ALA 20 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164 ARG* 3.1 20.3 + - - +
174 ARG* 3.2 6.9 + - - +
194 LYS* 1.3 74.1 - - - +
214 ILE* 1.3 61.2 + - + +
234 GLU* 3.4 7.6 + - - +
244 LYS* 2.9 49.1 + - + +
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Residues in contact with ILE 21 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174 ARG 3.2 13.6 + - - +
184 LEU* 3.5 7.2 - - - +
204 ALA* 1.3 75.3 - - + +
224 TYR* 1.3 59.2 + - - +
244 LYS* 3.2 15.3 + - + +
254 LYS* 2.9 49.9 + - + +
694 LEU* 4.2 19.5 - - + -
714 VAL* 4.1 19.5 - - + -
754 GLU* 4.1 38.1 - - + +
764 PHE* 4.4 13.9 - - + -
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Residues in contact with TYR 22 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232 T 2.7 28.6 + - - -
184 LEU 3.1 10.8 + - - +
194 LYS* 3.6 9.6 - - + +
204 ALA 3.2 0.2 - - - -
214 ILE* 1.3 77.2 - - - +
234 GLU* 1.3 76.6 + - - +
264 LYS* 2.8 57.5 + - + +
314 LEU* 4.0 13.2 - - + -
324 SER* 3.3 6.9 - - - -
334 GLN* 3.1 29.0 + - + -
364 VAL* 4.1 12.8 - - + -
514 PHE* 3.5 39.9 - + + -
694 LEU* 4.2 26.2 - - + -
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Residues in contact with GLU 23 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232 T 5.4 6.3 + - - +
242 A 4.7 3.3 + - - -
194 LYS* 2.9 50.5 + - + +
204 ALA* 3.7 8.5 - - - +
214 ILE 3.3 0.2 - - - -
224 TYR* 1.3 94.9 - - - +
244 LYS* 1.3 62.3 + - + +
254 LYS 3.2 0.5 + - - -
264 LYS* 3.6 31.5 + - - +
274 ASN* 4.8 2.6 + - - +
334 GLN* 5.6 1.2 + - - -
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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