Contacts of the helix formed by residues 214 - 228 (chain 2) 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 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1482 TRP* 3.8 9.7 + - - -
1722 ASN* 3.6 35.6 - - - +
1742 LEU* 3.4 36.0 + - - +
1752 MET* 3.7 23.2 - - + +
1782 VAL* 6.1 1.0 - - - +
2132 SER* 1.3 81.3 + - - +
2152 PRO* 1.3 75.1 - - + +
2172 GLY* 2.9 18.4 + - - -
2182 HIS* 4.0 31.0 + - + -
3132 ILE* 5.1 12.5 - - + +
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Residues in contact with PRO 215 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1722 ASN* 5.5 0.2 - - - +
2112 SER* 3.8 12.1 - - - +
2122 HIS 3.6 12.6 - - - +
2132 SER* 3.7 2.2 - - - -
2142 ARG* 1.3 95.0 - - + +
2162 VAL* 1.3 55.5 + - - +
2182 HIS* 2.7 37.8 + - + +
2192 CYS* 3.0 13.2 + - - -
2622 VAL* 4.0 17.0 - - + -
2632 GLU 4.2 1.6 - - - -
2642 GLY* 3.7 29.8 - - - +
3132 ILE* 5.8 5.4 - - + -
3142 PRO* 5.3 6.3 - - + +
3192 ILE* 5.7 0.2 - - + -
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Residues in contact with VAL 216 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1482 TRP* 3.6 34.1 - - + -
2012 GLU* 4.5 4.3 - - + -
2112 SER* 3.7 16.8 + - - +
2122 HIS* 3.6 28.3 - - - +
2132 SER 2.9 20.2 + - - +
2142 ARG 2.9 2.8 + - - -
2152 PRO* 1.3 74.1 - - - +
2172 GLY* 1.3 62.8 + - - +
2192 CYS* 3.3 5.1 + - - +
2202 LEU* 3.2 26.5 + - + +
2352 VAL* 4.9 5.6 - - + -
2372 ASN* 4.1 24.9 - - + +
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Residues in contact with GLY 217 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1482 TRP* 3.3 27.2 - - - +
2142 ARG 2.9 11.8 + - - -
2162 VAL* 1.3 78.6 - - - +
2182 HIS* 1.3 63.3 + - - +
2202 LEU* 3.5 4.7 + - - +
2212 GLU* 3.2 20.7 + - - +
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Residues in contact with HIS 218 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2142 ARG* 4.0 42.5 + - + +
2152 PRO* 2.7 25.5 + - + +
2172 GLY* 1.3 72.1 - - - +
2192 CYS* 1.3 55.8 + - - +
2212 GLU* 3.2 23.6 - - - +
2222 ALA* 2.7 29.8 + - - +
3132 ILE* 5.2 5.8 - - + +
3142 PRO* 3.8 21.2 + - - +
3152 GLN* 5.7 1.1 - - - -
3162 VAL* 3.5 22.3 - - + +
3192 ILE* 4.3 13.5 - - + +
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Residues in contact with CYS 219 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2092 VAL* 3.7 16.8 - - + -
2112 SER* 4.0 10.5 - - - -
2152 PRO 3.0 15.7 + - - -
2162 VAL* 3.4 8.5 - - - +
2182 HIS* 1.3 76.0 - - - +
2202 LEU* 1.3 55.8 + - - +
2212 GLU 2.9 1.3 - - - -
2222 ALA* 2.9 8.3 + - - +
2232 ALA* 2.8 34.8 + - - +
2352 VAL* 4.0 18.9 - - + +
2622 VAL* 3.7 34.1 - - - -
3192 ILE* 3.8 10.1 - - - -
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Residues in contact with LEU 220 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1482 TRP* 3.3 39.9 - - + -
2012 GLU* 3.7 29.2 - - + +
2022 ARG* 3.8 15.9 - - + -
2162 VAL* 3.2 10.0 + - + +
2172 GLY* 3.8 8.1 - - - +
2182 HIS 3.4 0.2 - - - -
2192 CYS* 1.3 78.7 - - - +
2212 GLU* 1.3 59.2 + - - +
2232 ALA* 3.3 18.1 - - - +
2242 ALA* 3.3 10.6 + - - +
2352 VAL* 3.7 23.3 - - + -
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Residues in contact with GLU 221 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2172 GLY 3.2 11.5 + - - +
2182 HIS* 3.2 27.6 - - - +
2192 CYS 2.9 0.4 - - - -
2202 LEU* 1.3 77.0 - - - +
2222 ALA* 1.3 62.4 + - - +
2232 ALA 3.2 0.2 - - - -
2242 ALA* 3.4 12.6 + - + +
2252 VAL* 3.5 17.6 + - + +
3162 VAL* 3.6 24.0 - - + +
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Residues in contact with ALA 222 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2182 HIS 2.7 16.5 + - - +
2192 CYS 2.9 7.4 + - - +
2212 GLU* 1.3 72.7 - - - +
2232 ALA* 1.3 64.6 + - - +
2252 VAL* 3.0 14.4 + - - +
2262 LEU* 3.1 23.8 + - + +
3162 VAL* 4.3 11.4 - - + +
3192 ILE* 4.1 27.1 - - + -
3202 ILE* 4.1 18.8 - - + +
3232 ILE* 5.0 2.9 - - + -
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Residues in contact with ALA 223 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2022 ARG* 3.4 35.4 + - - +
2192 CYS 2.8 11.6 + - - +
2202 LEU 3.3 13.0 - - - +
2222 ALA* 1.3 76.1 - - - +
2242 ALA* 1.3 63.3 + - - +
2262 LEU* 3.3 2.1 + - - +
2272 SER* 3.1 25.6 + - - -
2312 VAL 4.3 1.7 - - - +
2332 CYS* 4.1 20.8 - - + -
2352 VAL* 4.1 9.6 - - + -
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Residues in contact with ALA 224 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2022 ARG* 5.3 2.9 - - - +
2202 LEU 3.3 9.5 + - - +
2212 GLU* 3.8 10.5 - - + +
2222 ALA 3.1 0.6 - - - -
2232 ALA* 1.3 79.3 - - - +
2252 VAL* 1.3 65.2 + - + +
2262 LEU 3.5 0.3 + - - -
2272 SER* 3.6 6.9 + - - -
2282 LYS* 3.6 23.5 + - - +
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Residues in contact with VAL 225 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2212 GLU* 3.5 17.7 + - + +
2222 ALA* 3.0 7.3 + - - +
2242 ALA* 1.3 76.5 - - + +
2262 LEU* 1.3 63.6 + - + +
2282 LYS* 3.4 30.4 + - - +
2292 GLU* 3.8 17.7 - - - +
3162 VAL* 5.0 5.4 - - + -
3202 ILE* 3.8 28.9 - - + -
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Residues in contact with LEU 226 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2222 ALA* 3.1 23.2 + - + +
2232 ALA 4.0 1.6 - - - +
2252 VAL* 1.3 78.9 - - + +
2272 SER* 1.3 59.1 + - - +
2282 LYS 3.3 0.2 - - - -
2292 GLU* 3.0 28.1 + - - +
2312 VAL* 3.1 36.0 + - + +
2332 CYS* 3.6 26.2 - - - -
3202 ILE* 3.8 30.7 - - + -
3232 ILE* 3.7 30.7 - - + -
3242 LYS* 4.2 24.2 - - + -
3292 ILE* 5.1 0.2 - - + -
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Residues in contact with SER 227 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2022 ARG* 3.6 18.3 + - - -
2232 ALA 3.1 9.8 + - - -
2242 ALA* 3.6 5.7 + - - -
2252 VAL 3.3 0.4 - - - -
2262 LEU* 1.3 76.1 - - - +
2282 LYS* 1.3 56.6 + - - +
2292 GLU 2.8 8.6 + - - -
2302 GLY* 3.3 9.2 + - - -
2312 VAL 3.5 15.7 - - - +
2322 GLU* 3.4 24.9 + - - -
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Residues in contact with LYS 228 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2242 ALA* 3.6 16.0 + - - +
2252 VAL* 3.4 21.0 + - - +
2262 LEU 3.3 0.4 - - - -
2272 SER* 1.3 76.6 + - - +
2292 GLU* 1.3 63.8 + - + +
2302 GLY 3.7 0.2 - - - -
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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