Contacts of the helix formed by residues 214 - 228 (chain 4) in PDB entry 3EXG
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 ARG 214 (chain 4).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1204 ALA* 5.4 3.0 + - - +
1484 TRP* 4.0 12.1 + - - -
1724 ASN* 3.4 34.8 - - - +
1744 LEU* 3.8 33.3 - - - +
1754 MET* 4.2 16.5 - - - +
2134 SER* 1.3 79.2 + - - +
2154 PRO* 1.4 62.4 - - + +
2164 VAL 2.7 11.6 + - - -
2174 GLY* 2.9 15.4 + - - -
2184 HIS* 3.5 34.6 + - + -
3134 ILE* 4.1 26.7 - - - +
3154 GLN* 6.1 0.6 - - - +
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Residues in contact with PRO 215 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1724 ASN* 5.4 0.2 - - - +
2114 SER* 3.7 11.7 - - - +
2124 HIS* 3.4 17.9 - - + +
2134 SER* 3.4 2.9 - - - +
2144 ARG* 1.4 96.5 - - + +
2164 VAL* 1.3 60.1 + - - -
2174 GLY 3.2 0.7 - - - -
2184 HIS* 3.1 19.0 + - + +
2194 CYS* 3.1 23.4 + - - -
2624 VAL* 3.8 14.5 - - + +
2634 GLU 4.4 0.9 - - - -
2644 GLY* 4.2 25.1 - - - +
3134 ILE* 6.2 3.4 - - + -
3144 PRO* 4.7 10.5 - - + -
3194 ILE* 5.6 0.2 - - + -
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Residues in contact with VAL 216 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1484 TRP* 3.5 38.6 - - + -
2014 GLU* 4.7 2.9 - - + -
2114 SER* 3.5 39.7 + - - +
2124 HIS* 3.7 5.2 - - - +
2134 SER 2.6 26.0 + - - +
2144 ARG 2.7 1.6 + - - -
2154 PRO* 1.3 70.5 - - - +
2174 GLY* 1.3 62.8 + - - +
2194 CYS* 3.0 14.8 + - - +
2204 LEU* 3.0 18.4 + - + +
2354 VAL* 4.9 5.6 - - + -
2364 ILE 4.7 0.7 - - - +
2374 ASN* 4.1 23.6 - - + +
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Residues in contact with GLY 217 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1484 TRP* 3.5 25.2 - - - +
2144 ARG 2.9 10.3 + - - -
2164 VAL* 1.3 80.4 - - - +
2184 HIS* 1.3 56.3 + - - +
2204 LEU* 3.2 6.2 + - - +
2214 GLU* 3.0 29.4 + - - +
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Residues in contact with HIS 218 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2144 ARG* 3.5 45.3 + - + +
2154 PRO* 3.1 24.4 + - + +
2174 GLY* 1.3 77.6 - - - +
2194 CYS* 1.3 56.6 + - - +
2214 GLU* 3.3 13.6 + - - +
2224 ALA* 3.0 27.4 + - - +
3134 ILE* 5.3 2.1 - - + +
3144 PRO 4.2 18.6 + - - +
3154 GLN* 5.6 4.9 + - - -
3164 VAL* 3.6 28.9 - - + +
3194 ILE* 3.7 18.5 - - + +
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Residues in contact with CYS 219 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2094 VAL* 3.9 15.2 - - + +
2114 SER* 3.7 18.2 - - - -
2154 PRO 3.1 18.2 + - - -
2164 VAL 3.0 7.9 + - - +
2184 HIS* 1.3 73.5 - - - +
2204 LEU* 1.3 59.3 + - - +
2224 ALA* 3.1 6.6 + - - +
2234 ALA* 3.0 27.2 + - - +
2354 VAL* 3.9 21.7 - - + +
2624 VAL* 3.7 32.5 - - - -
3194 ILE* 4.1 7.9 - - - -
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Residues in contact with LEU 220 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1484 TRP* 3.3 39.7 - - + -
2014 GLU* 4.1 18.4 - - + +
2024 ARG* 4.0 31.1 - - + -
2164 VAL* 3.0 12.6 + - + +
2174 GLY* 3.2 8.5 + - - +
2194 CYS* 1.3 75.8 - - - +
2214 GLU* 1.3 62.3 + - - +
2234 ALA* 3.4 6.6 + - - +
2244 ALA* 3.3 18.5 + - - +
2354 VAL* 4.2 14.6 - - + -
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Residues in contact with GLU 221 (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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2174 GLY 3.0 13.3 + - - +
2184 HIS* 3.4 19.3 - - - +
2194 CYS 3.1 0.2 - - - -
2204 LEU* 1.3 78.2 - - - +
2224 ALA* 1.3 60.7 + - - +
2244 ALA* 3.3 16.3 + - + +
2254 VAL* 3.4 18.5 + - + +
3164 VAL* 3.7 24.5 - - + +
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Residues in contact with ALA 222 (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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2184 HIS 3.0 13.1 + - - +
2194 CYS 3.1 8.5 + - - +
2214 GLU* 1.3 76.7 - - - +
2234 ALA* 1.3 57.5 + - - +
2254 VAL* 3.6 1.2 + - - +
2264 LEU* 3.0 37.3 + - + +
2334 CYS* 5.7 0.2 - - - -
3164 VAL* 3.8 13.9 - - + +
3194 ILE* 3.8 21.1 - - + -
3204 ILE* 3.6 23.9 - - + +
3234 ILE* 5.3 1.8 - - + -
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Residues in contact with ALA 223 (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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2024 ARG* 3.3 40.8 + - - +
2194 CYS 3.0 11.6 + - - +
2204 LEU 3.5 9.6 - - - +
2214 GLU 3.2 0.4 - - - -
2224 ALA* 1.3 73.6 - - - +
2244 ALA* 1.3 60.3 + - - +
2264 LEU* 3.3 5.6 + - - +
2274 SER* 2.9 33.3 + - - -
2314 VAL 4.7 0.3 - - - +
2334 CYS* 4.2 18.7 - - + +
2354 VAL* 4.4 2.7 - - + -
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Residues in contact with ALA 224 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2024 ARG* 5.1 1.1 - - - +
2204 LEU 3.3 7.9 + - - +
2214 GLU* 3.3 12.7 + - + +
2234 ALA* 1.3 79.0 - - - +
2254 VAL* 1.3 65.4 + - + +
2274 SER* 3.4 9.6 + - - -
2284 LYS* 2.9 32.0 + - - +
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Residues in contact with VAL 225 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2214 GLU* 3.4 16.0 + - + +
2224 ALA 4.0 1.1 - - - +
2234 ALA 3.3 0.6 - - - -
2244 ALA* 1.3 77.6 - - + +
2264 LEU* 1.3 66.5 + - + +
2284 LYS* 3.3 20.0 + - - +
2294 GLU* 4.0 18.0 - - - +
3164 VAL* 5.0 4.5 - - + -
3204 ILE* 3.8 31.0 - - + -
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Residues in contact with LEU 226 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2224 ALA 3.0 20.5 + - - +
2234 ALA* 3.8 5.2 - - - +
2254 VAL* 1.3 80.1 - - - +
2274 SER* 1.3 61.6 + - - +
2294 GLU* 3.1 36.5 + - - +
2304 GLY 3.5 0.2 + - - -
2314 VAL* 3.5 37.0 + - + +
2334 CYS* 4.2 7.9 - - - -
3204 ILE* 4.3 26.5 - - + -
3234 ILE* 3.7 44.0 - - + -
3244 LYS* 4.7 9.9 - - + -
3294 ILE* 4.9 0.2 - - + -
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Residues in contact with SER 227 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2024 ARG* 3.7 12.9 + - - -
2234 ALA 2.9 20.2 + - - -
2244 ALA* 3.4 4.9 + - - -
2254 VAL 3.3 0.4 - - - -
2264 LEU* 1.3 69.5 - - - +
2284 LYS* 1.3 60.6 + - - +
2294 GLU 2.9 5.2 - - - -
2304 GLY* 2.9 16.3 + - - -
2314 VAL 3.4 15.0 - - - +
2324 GLU* 3.2 25.6 + - - +
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Residues in contact with LYS 228 (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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2244 ALA* 2.9 32.2 + - - +
2254 VAL* 3.3 11.7 + - - +
2264 LEU 3.1 1.6 - - - -
2274 SER* 1.3 79.6 - - - +
2294 GLU* 1.3 62.5 + - + +
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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
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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