Contacts of the helix formed by residues 219 - 228 (chain B) in PDB entry 2IT4
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* 3.9 2.0 - - - -
151B GLY 3.5 9.4 - - - -
152B GLU 3.6 1.0 + - - -
153B ALA* 3.4 28.6 - - - +
218B VAL* 1.3 76.4 - - - +
220B SER* 1.3 64.4 + - - +
221B GLU* 3.5 16.6 + - - +
222B GLN* 2.9 40.3 + - - +
223B LEU* 3.2 23.6 + - - +
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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 ASN* 2.4 41.5 + - - +
150B VAL* 3.6 14.7 - - - +
151B GLY 4.4 1.8 + - - -
219B SER* 1.3 73.3 - - - +
221B GLU* 1.3 74.8 + - - +
223B LEU* 3.5 6.2 + - - +
224B ALA* 3.2 23.4 + - - +
227B ARG* 4.8 0.3 + - - -
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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* 3.2 15.1 + - - +
220B SER* 1.3 89.6 - - - +
222B GLN* 1.3 61.5 + - + +
224B ALA* 3.3 10.3 + - - +
225B GLN* 3.1 30.7 + - - +
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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* 3.9 7.8 - - + +
154B ASN* 2.9 52.2 + - - +
157B LEU* 4.1 4.8 - - + +
158B GLN* 4.7 3.8 - - - +
161B LEU* 3.5 35.5 - - + +
218B VAL* 3.7 12.2 - - + +
219B SER* 2.9 39.5 + - - +
221B GLU* 1.3 75.8 - - + +
223B LEU* 1.3 62.9 + - - +
225B GLN* 3.2 24.0 + - - +
226B PHE* 3.4 12.3 + - + -
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Residues in contact with LEU 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* 4.7 5.1 - - + -
101B ASN* 3.6 43.1 - - + +
115B SER* 4.1 10.5 - - - +
116B ALA* 3.7 28.3 - - + -
150B VAL* 4.1 6.5 - - + -
218B VAL* 3.7 31.6 - - + -
219B SER 3.2 14.4 + - - +
220B SER 3.8 1.6 - - - +
222B GLN* 1.3 74.6 - - - +
224B ALA* 1.3 62.6 + - - +
226B PHE* 3.2 37.0 - - + +
227B ARG* 3.2 22.5 + - - +
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Residues in contact with ALA 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 3.2 14.1 + - - +
221B GLU* 3.4 13.0 - - - +
222B GLN 3.2 0.4 - - - -
223B LEU* 1.3 75.1 - - - +
225B GLN* 1.3 63.7 + - - +
227B ARG* 3.3 18.7 + - - +
228B SER* 3.1 26.0 + - - -
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Residues in contact with GLN 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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161B LEU* 3.7 53.6 + - + +
162B ASP* 5.1 4.6 + - - +
164B LEU* 3.7 16.8 - - + +
168B LYS* 5.2 1.0 + - - -
221B GLU 3.1 16.3 + - - +
222B GLN* 3.2 14.8 + - - +
224B ALA* 1.3 72.8 - - - +
226B PHE* 1.3 66.8 + - - +
228B SER* 3.2 21.4 + - - -
229B LEU* 3.8 2.1 + - - +
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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* 3.9 29.8 - + - -
95B PHE* 3.6 36.3 - + + -
97B TRP* 3.5 50.4 - + + -
116B ALA* 4.7 5.4 - - + -
148B MET* 4.8 5.8 - - + -
157B LEU* 4.5 9.4 - - + -
161B LEU* 3.9 23.6 - - + -
164B LEU* 4.3 4.7 - - + -
218B VAL* 5.1 1.3 - - + -
222B GLN 3.4 2.8 + - - -
223B LEU* 3.2 41.2 + - + +
225B GLN* 1.3 77.1 - - - +
227B ARG* 1.3 56.5 + - - +
228B SER 3.1 0.2 - - - -
229B LEU* 3.2 26.7 + - - +
241B MET 4.1 0.5 - - - +
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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* 3.7 18.9 - - + +
98B GLY 2.7 26.1 + - - +
99B SER* 3.5 15.2 + - - +
100B THR* 3.4 15.7 + - - -
101B ASN* 2.8 29.7 + - - +
220B SER 4.8 0.4 + - - -
223B LEU* 3.2 35.1 + - - +
224B ALA* 3.3 18.6 + - - +
226B PHE* 1.3 76.3 - - - +
228B SER* 1.3 61.2 + - - +
229B LEU 3.2 4.0 + - - +
240B PRO* 3.5 24.6 - - - +
241B MET 3.3 11.9 + - - +
242B GLN* 3.4 28.0 + - - +
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Residues in contact with SER 228 (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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168B LYS* 3.4 30.1 + - - +
224B ALA 3.1 13.2 + - - -
225B GLN* 3.4 14.9 - - - -
226B PHE 3.1 0.4 - - - -
227B ARG* 1.3 74.3 - - - +
229B LEU* 1.3 66.3 + - - +
230B LEU* 3.6 10.9 - - - +
240B PRO* 5.5 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