Contacts of the helix formed by residues 221 - 231 (chain A) in PDB entry 4LVB
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 VAL 221 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195A TYR* 4.4 1.6 - - + -
219A ASP 3.6 0.9 - - - +
220A THR* 1.3 69.7 - - - +
222A ALA* 1.3 65.0 + - - +
223A GLY 3.2 0.2 - - - -
224A LEU* 3.1 35.1 + - + +
225A ALA* 3.7 4.0 + - - +
13B LEU* 3.6 26.0 - - + +
15B THR 3.4 24.5 - - - +
17B SER* 3.8 18.4 - - - +
86B VAL* 4.0 21.5 - - + -
87B TYR* 4.0 30.5 - - + +
90B HIS* 5.2 2.2 - - + -
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Residues in contact with ALA 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A TYR* 4.2 21.2 - - + +
201A GLN* 4.7 6.1 - - - +
204A ALA 4.6 1.1 - - - -
205A GLY* 3.7 23.8 - - - +
220A THR* 3.1 2.1 + - - +
221A VAL* 1.3 75.7 - - - +
223A GLY* 1.3 66.6 + - - +
224A LEU 3.2 0.3 + - - -
225A ALA* 3.3 8.3 + - - +
226A LEU* 3.3 22.2 + - - +
13B LEU 4.6 3.8 + - - +
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Residues in contact with GLY 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A GLY* 3.5 22.6 - - - -
208A ALA* 3.7 15.6 - - - +
209A SER* 4.1 4.2 - - - -
212A LEU* 4.7 1.8 - - - -
220A THR 3.2 6.9 + - - -
221A VAL 3.2 1.2 - - - -
222A ALA* 1.3 78.6 - - - +
224A LEU* 1.3 62.8 + - - +
226A LEU* 3.5 3.0 + - - +
227A ILE* 3.1 32.4 + - - +
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Residues in contact with LEU 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A LEU* 4.1 5.6 - - + -
218A THR* 3.9 28.0 - - + -
220A THR 4.7 1.6 - - - +
221A VAL* 3.1 29.6 + - + +
223A GLY* 1.3 76.3 - - - +
225A ALA* 1.3 62.3 + - - +
227A ILE* 3.2 4.7 + - - +
228A LYS* 3.1 23.1 + - - +
237A VAL* 4.1 21.3 - - + -
238A PRO* 4.1 17.5 - - + +
239A GLY* 4.0 21.8 - - - +
86B VAL* 4.2 10.8 - - + -
90B HIS* 3.6 28.0 - - + +
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Residues in contact with ALA 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A VAL 3.7 4.8 + - - +
222A ALA* 3.3 11.0 + - - +
224A LEU* 1.3 78.5 - - - +
226A LEU* 1.3 63.6 + - - +
228A LYS* 3.3 9.4 + - - +
229A LYS* 3.0 26.4 + - - +
13B LEU* 6.2 4.0 - - + -
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Residues in contact with LEU 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A TYR* 4.2 8.1 - - - +
64A TYR* 3.5 41.1 - - + +
202A GLU 5.3 0.2 - - - +
205A GLY* 3.8 4.0 - - - +
206A ILE* 3.6 37.2 - - + +
209A SER* 3.8 19.3 - - - +
222A ALA 3.3 11.4 + - - +
223A GLY 3.7 8.3 - - - +
225A ALA* 1.3 78.7 - - - +
227A ILE* 1.3 64.0 + - - +
229A LYS* 3.3 0.4 + - - -
230A TYR* 2.9 40.2 + - + +
231A TYR* 4.3 11.4 - - + -
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Residues in contact with ILE 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A TYR* 4.5 1.8 - - - +
209A SER* 3.7 19.3 - - - -
212A LEU* 3.6 18.4 - - + -
223A GLY 3.1 11.7 + - - +
224A LEU 3.2 6.3 + - - +
226A LEU* 1.3 77.7 - - - +
228A LYS* 1.3 53.5 + - - +
231A TYR* 2.8 15.1 + - + -
232A GLY 2.7 29.7 + - - +
233A THR* 4.0 16.6 - - + +
238A PRO* 3.6 27.4 - - + -
473A PHE* 3.5 57.2 - - + -
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Residues in contact with LYS 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A LEU 3.1 12.4 + - - +
225A ALA* 3.3 11.9 + - - +
227A ILE* 1.3 80.7 - - - +
229A LYS* 1.3 61.5 + - - +
231A TYR 4.3 0.5 + - - -
232A GLY* 3.9 16.8 + - - +
233A THR* 5.4 2.0 - - - +
236A PRO 5.1 13.5 + - - +
238A PRO* 5.9 1.3 - - + +
86B VAL* 6.2 1.8 - - - +
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Residues in contact with LYS 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A ALA 3.0 17.5 + - - +
226A LEU* 4.0 2.2 - - - +
228A LYS* 1.3 80.1 - - + +
230A TYR* 1.3 97.4 + - + +
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Residues in contact with TYR 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A GLN* 2.8 24.9 + - - +
64A TYR* 3.5 37.7 - + - +
67A ASN* 3.7 35.5 + - + +
68A LYS* 3.6 43.2 + - + +
226A LEU* 2.9 30.5 + - + +
229A LYS* 1.3 117.7 + - + +
231A TYR* 1.3 77.0 + - + +
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Residues in contact with TYR 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A TYR* 3.5 26.7 - + - -
61A GLY* 3.4 19.1 - - - -
63A GLN* 3.4 31.3 + - + +
64A TYR* 3.4 15.8 + - + -
121A GLU* 2.9 28.2 + - - -
226A LEU* 4.3 12.8 - - + -
227A ILE* 2.8 11.1 + - - +
228A LYS 4.6 0.9 - - - -
229A LYS 3.7 0.4 - - - -
230A TYR* 1.3 94.9 - - + +
232A GLY* 1.3 62.3 + - - +
471A TYR 3.5 7.2 - - - +
472A SER* 3.4 15.8 - - - -
473A PHE* 3.9 24.9 - + + +
476A ILE* 3.4 23.6 - - + -
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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