Contacts of the helix formed by residues 207 - 226 (chain 5) in PDB entry 5LN3
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 GLU 207 (chain 5).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675 PHE* 4.3 2.5 - - - -
685 ARG* 3.5 23.2 + - - +
2065 LEU* 1.3 81.6 - - - +
2085 VAL* 1.3 63.3 + - + +
2095 GLU* 4.4 14.0 - - - +
2105 GLN* 3.2 33.2 + - + +
2115 ALA* 3.0 23.6 + - - +
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Residues in contact with VAL 208 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675 PHE* 3.9 19.7 - - + -
695 HIS* 6.0 5.4 - - + +
2075 GLU* 1.3 71.7 - - + +
2095 GLU* 1.3 87.6 + - + +
2115 ALA* 3.3 9.1 + - - +
2125 TYR* 3.3 35.6 + - + +
2375 HIS* 3.9 28.7 - - + +
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Residues in contact with GLU 209 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2075 GLU* 3.4 13.8 - - - +
2085 VAL* 1.3 100.7 - - + +
2105 GLN* 1.4 70.8 - - - +
2125 TYR* 3.3 37.5 + - + +
2135 ASP* 3.3 19.2 + - - +
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Residues in contact with GLN 210 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2065 LEU* 3.7 17.6 - - + +
2075 GLU* 3.2 38.0 + - + +
2095 GLU* 1.4 81.9 - - - +
2115 ALA* 1.3 63.9 + - - +
2135 ASP* 3.1 19.6 + - - +
2145 LEU* 3.0 19.4 + - - +
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Residues in contact with ALA 211 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655 PHE* 3.8 12.2 - - + -
675 PHE* 4.5 5.6 - - + -
725 ILE* 3.9 22.6 - - + +
2065 LEU* 3.7 21.3 - - + +
2075 GLU 3.0 12.6 + - - +
2085 VAL* 3.3 12.3 + - - +
2105 GLN* 1.3 74.2 - - - +
2125 TYR* 1.3 65.2 + - - +
2145 LEU* 2.9 20.3 + - - +
2155 ALA* 3.1 10.9 + - - +
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Residues in contact with TYR 212 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725 ILE* 4.2 22.9 - - + -
2085 VAL* 3.3 34.1 - - + +
2095 GLU* 3.4 39.2 + - - +
2105 GLN 3.3 0.4 - - - -
2115 ALA* 1.3 76.7 - - - +
2135 ASP* 1.4 62.9 + - - +
2155 ALA* 3.6 5.9 + - - +
2165 ARG* 3.1 43.4 + - - +
2355 LEU* 4.3 7.9 - - + +
2375 HIS* 4.3 11.4 - + + +
2445 ILE* 5.8 1.9 - - - +
2465 VAL* 3.4 49.3 - - + +
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Residues in contact with ASP 213 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2095 GLU* 3.3 19.0 + - - +
2105 GLN* 3.1 21.3 + - - +
2125 TYR* 1.4 75.7 - - - +
2145 LEU* 1.4 56.7 + - - +
2165 ARG* 3.4 25.0 + - - +
2175 ARG* 3.0 43.3 + - - +
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Residues in contact with LEU 214 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655 PHE* 4.3 19.5 - - + -
1975 VAL* 3.4 33.4 - - + +
1985 MET* 4.2 15.0 - - + +
2015 GLY* 3.9 32.1 - - - -
2025 TYR* 5.2 1.1 - - - -
2065 LEU* 4.3 20.2 - - + -
2105 GLN 3.0 11.3 + - - +
2115 ALA* 2.9 13.5 + - - +
2135 ASP* 1.4 60.0 - - - +
2155 ALA* 1.3 63.5 + - - +
2175 ARG* 3.8 1.8 + - - +
2185 ALA* 3.3 20.6 + - - +
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Residues in contact with ALA 215 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635 LEU* 4.2 5.3 - - + +
655 PHE* 4.2 18.8 - - + -
725 ILE* 4.7 2.7 - - + -
745 ALA* 4.0 13.7 - - + -
1985 MET* 6.4 0.9 - - - -
2115 ALA 3.1 8.4 + - - +
2125 TYR 3.9 3.1 - - - +
2145 LEU* 1.3 80.7 - - - +
2165 ARG* 1.4 62.1 + - - +
2185 ALA* 3.1 8.8 + - - +
2195 ILE* 3.1 26.4 + - - +
2355 LEU* 3.6 26.7 - - + -
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Residues in contact with ARG 216 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2125 TYR* 3.1 54.0 + - - +
2135 ASP* 3.2 25.1 + - - +
2155 ALA* 1.4 78.4 - - - +
2175 ARG* 1.4 62.4 + - - +
2195 ILE* 3.3 15.5 + - - +
2205 TYR* 3.4 11.3 + - - +
2335 VAL* 5.0 17.5 - - + +
2355 LEU* 3.5 17.1 - - + +
2465 VAL* 4.6 9.5 + - - +
2495 ASP* 2.9 46.7 + - + +
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Residues in contact with ARG 217 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1975 VAL* 4.8 12.3 - - + +
2135 ASP* 3.0 24.3 + - - +
2145 LEU* 4.2 3.6 - - - +
2165 ARG* 1.4 76.3 - - - +
2185 ALA* 1.4 58.4 + - - +
2205 TYR* 3.1 30.3 + - - +
2215 GLN* 3.3 12.6 + - - +
2545 LEU* 5.0 19.5 - - - +
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Residues in contact with ALA 218 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635 LEU* 4.1 17.3 - - + -
1945 ALA* 4.0 23.1 - - - +
1975 VAL* 3.9 28.4 - - + +
1985 MET* 5.0 3.8 - - + +
2145 LEU 3.3 12.9 + - - +
2155 ALA* 3.1 10.9 + - - +
2175 ARG* 1.4 78.7 - - - +
2195 ILE* 1.4 61.8 - - - +
2215 GLN* 3.7 11.1 + - - +
2225 ALA* 3.7 10.0 + - - +
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Residues in contact with ILE 219 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615 THR* 3.9 31.6 - - + +
635 LEU* 4.2 23.6 - - + -
745 ALA* 5.0 6.1 - - + +
755 ALA* 5.4 1.3 - - - -
765 ASP* 4.5 15.9 - - + +
1945 ALA* 5.4 0.9 - - + -
2155 ALA 3.1 14.0 + - - +
2165 ARG 3.7 7.4 - - - +
2175 ARG 3.3 0.6 - - - -
2185 ALA* 1.4 76.9 - - - +
2205 TYR* 1.4 62.8 + - - +
2225 ALA* 3.1 22.1 + - + +
2235 THR* 3.3 7.9 + - - +
2295 SER* 5.9 0.9 - - - -
2305 GLY 5.0 4.5 - - - +
2335 VAL* 3.7 37.2 - - + -
2515 VAL* 4.6 12.8 - - + -
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Residues in contact with TYR 220 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2165 ARG 3.4 8.9 + - - +
2175 ARG* 3.1 21.2 + - - +
2195 ILE* 1.4 76.1 - - - +
2215 GLN* 1.3 61.3 + - - +
2235 THR* 3.2 22.3 + - + -
2245 TYR* 4.1 18.6 + + - -
2515 VAL* 3.4 45.2 + - + -
2525 ALA* 4.2 3.5 - - - -
2535 ASP 4.0 4.7 + - - -
2545 LEU* 3.6 44.3 + - + -
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Residues in contact with GLN 221 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1935 TYR* 3.7 23.5 - - + +
1975 VAL* 3.2 27.9 - - + +
2175 ARG 3.3 8.6 + - - +
2185 ALA 3.7 11.4 - - - +
2195 ILE 3.2 0.2 - - - -
2205 TYR* 1.3 78.6 - - - +
2225 ALA* 1.4 58.1 + - - +
2235 THR 3.4 0.3 + - - -
2245 TYR* 3.6 13.0 + - - +
2255 ARG* 3.6 19.0 - - - +
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Residues in contact with ALA 222 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615 THR* 4.2 22.9 - - + +
1905 GLY* 4.7 11.9 - - - +
1935 TYR* 5.1 4.0 - - + +
1945 ALA* 5.8 1.3 - - + -
2185 ALA 3.7 6.7 + - - +
2195 ILE* 3.1 19.9 + - + +
2215 GLN* 1.4 74.0 - - - +
2235 THR* 1.4 57.9 + - - +
2255 ARG* 3.2 11.8 + - - +
2265 ASP* 3.1 29.2 + - - +
2295 SER* 4.1 12.8 - - - +
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Residues in contact with THR 223 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
785 ARG* 6.0 1.6 - - - +
2195 ILE 3.3 8.3 + - - -
2205 TYR* 3.2 21.9 + - + -
2225 ALA* 1.4 72.0 - - - +
2245 TYR* 1.4 65.1 + - + +
2265 ASP 3.0 20.5 - - - +
2275 ALA* 4.9 1.4 - - - -
2295 SER* 4.8 7.1 - - - +
2305 GLY* 4.1 15.6 - - - -
2315 GLY 5.6 0.4 - - - +
2515 VAL* 3.2 32.2 - - + +
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Residues in contact with TYR 224 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2205 TYR* 4.6 20.4 - + - -
2215 GLN* 3.6 9.7 + - - +
2225 ALA 3.4 0.4 - - - -
2235 THR* 1.4 82.0 - - + +
2255 ARG* 1.4 76.1 + - - +
2265 ASP 3.8 0.9 + - - -
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Residues in contact with ARG 225 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1905 GLY* 5.4 3.8 - - - -
1935 TYR* 3.1 66.7 + - + -
2215 GLN* 3.6 23.1 - - - +
2225 ALA* 3.2 10.1 + - - +
2245 TYR* 1.4 92.1 + - - +
2265 ASP* 1.4 61.9 + - + +
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Residues in contact with ASP 226 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605 THR 3.1 22.9 + - - -
1895 SER* 2.9 29.4 + - - +
1905 GLY* 5.3 4.0 - - - +
2225 ALA 3.1 8.8 + - - +
2235 THR 3.0 18.3 - - - +
2245 TYR 4.9 0.9 - - - -
2255 ARG* 1.4 81.4 - - + +
2275 ALA* 1.3 63.9 + - - +
2285 TYR* 3.3 18.5 + - - +
2295 SER* 3.3 21.5 + - - +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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