Contacts of the helix formed by residues 219 - 227 (chain B) in PDB entry 3V3H
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 SER 219 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150B VAL* 4.2 1.3 - - - -
151B GLY 3.4 14.6 - - - -
152B SER 3.5 1.8 + - - -
153B ALA* 3.9 17.8 - - - +
218B VAL* 1.3 77.5 - - - +
220B SER* 1.3 65.4 + - - +
221B GLU* 3.5 18.7 + - - +
222B GLN* 3.1 43.7 + - - +
223B VAL* 3.2 14.7 + - - +
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Residues in contact with SER 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B ASP* 4.4 9.1 + - - -
150B VAL* 3.7 23.1 - - - +
151B GLY 4.6 0.8 + - - -
219B SER* 1.3 75.1 - - - +
221B GLU* 1.3 59.8 + - - +
223B VAL* 3.5 7.3 - - - +
224B SER* 2.9 32.7 + - - -
227B ARG* 5.2 0.9 + - - -
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Residues in contact with GLU 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B SER* 3.5 19.6 + - - +
220B SER* 1.3 80.2 - - - +
222B GLN* 1.3 60.7 + - - +
224B SER* 2.8 21.6 + - - -
225B LYS* 3.2 19.2 + - - +
302B CL 3.8 15.7 - - + -
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Residues in contact with GLN 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B ALA* 3.6 5.5 - - + +
154B LYS* 3.0 45.8 + - - +
155B PRO* 5.0 0.2 - - - +
157B LEU* 4.0 19.6 - - + +
158B GLN* 2.8 38.4 + - - +
161B VAL* 3.5 27.4 - - + +
218B VAL* 3.4 8.4 - - + +
219B SER* 3.1 34.5 + - - +
221B GLU* 1.3 77.1 - - - +
223B VAL* 1.3 61.6 + - - +
225B LYS* 3.3 11.7 + - - +
226B PHE* 3.8 2.8 + - - -
302B CL 3.9 10.8 - - + -
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Residues in contact with VAL 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B TRP* 4.8 4.0 - - + -
101B ASP* 3.7 22.4 - - - +
115B ALA* 4.5 19.5 - - + +
116B ALA* 4.6 6.7 - - + -
148B LEU* 5.6 0.2 - - + -
150B VAL* 4.0 12.6 - - + -
157B LEU* 6.2 0.4 - - - -
218B VAL* 4.3 14.1 - - + +
219B SER 3.2 9.6 + - - +
220B SER* 3.5 10.5 - - - +
222B GLN* 1.3 77.2 - - - +
224B SER* 1.3 66.2 + - - +
226B PHE* 2.9 46.8 + - + +
227B ARG* 3.7 19.9 + - - +
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Residues in contact with SER 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220B SER* 2.9 19.8 + - - -
221B GLU* 2.8 24.9 + - - -
223B VAL* 1.3 77.8 - - - +
225B LYS* 1.3 59.9 + - - +
227B ARG* 3.1 37.2 + - - +
228B LYS* 3.6 24.3 + - - +
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Residues in contact with LYS 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B GLN* 4.1 0.2 - - - +
161B VAL* 3.7 37.7 - - + +
162B ASP* 2.8 28.3 + - - +
164B LEU* 3.8 13.4 - - + +
221B GLU* 3.2 12.3 + - - +
222B GLN 3.5 8.3 - - - +
223B VAL 3.2 0.6 - - - -
224B SER* 1.3 72.8 - - - +
226B PHE* 1.3 65.2 + - - +
228B LYS* 3.2 36.3 + - + +
229B LEU* 3.9 3.1 + - - +
302B CL 3.5 23.4 - - + +
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Residues in contact with PHE 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B PHE* 4.0 17.9 - + - -
95B PHE* 3.8 47.6 - + + -
97B TRP* 3.4 52.7 + + + +
116B ALA* 4.6 3.6 - - + -
148B LEU* 4.4 11.0 - - + -
157B LEU* 4.5 8.3 - - + -
160B VAL* 4.7 2.5 - - + -
161B VAL* 3.6 26.5 - - + -
164B LEU* 3.5 16.6 - - + -
222B GLN 4.2 2.5 - - - -
223B VAL* 2.9 25.5 + - + +
225B LYS* 1.3 75.8 - - - +
227B ARG* 1.3 59.4 + - - +
229B LEU* 3.3 22.5 + - - +
241B MET 3.6 0.7 - - - +
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Residues in contact with ARG 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B TRP* 4.0 7.7 - - + -
98B GLY 3.0 26.8 + - - +
99B SER 3.8 14.4 + - - -
100B HIS* 3.3 26.2 + - - +
101B ASP* 2.8 31.5 + - - +
115B ALA* 5.1 3.6 + - - +
220B SER* 5.2 0.8 + - - -
223B VAL* 3.9 25.0 - - - +
224B SER* 3.1 32.4 + - - +
226B PHE* 1.3 76.0 - - - +
228B LYS* 1.3 60.4 + - - +
229B LEU 3.3 7.5 - - - +
240B PRO* 3.8 17.7 - - - +
241B MET 3.8 7.9 - - - -
242B VAL* 3.7 12.9 - - + +
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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