Contacts of the helix formed by residues 168 - 182 (chain B) in PDB entry 3F22
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 PRO 168 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B SER* 4.2 0.9 - - - +
166B GLY 4.7 0.7 - - - +
167B THR* 1.3 91.0 - - + +
169B LYS* 1.3 67.0 + - - +
170B LYS* 4.3 6.1 - - + +
171B GLU* 2.9 36.7 + - + +
172B ILE* 2.9 21.5 + - - +
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Residues in contact with LYS 169 (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 ALA* 4.0 12.6 - - + -
159B HIS* 3.8 40.2 - - + +
162B SER* 3.5 15.2 + - - +
167B THR 3.3 3.6 + - - -
168B PRO* 1.3 70.9 - - - +
170B LYS* 1.3 57.3 + - - +
172B ILE* 3.4 8.2 - - - +
173B ASN* 2.8 39.7 + - - +
3E T 4.9 9.4 + - - +
4E A 3.2 19.5 + - - -
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Residues in contact with LYS 170 (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 PRO* 3.0 6.4 - - + +
169B LYS* 1.3 80.2 - - - +
171B GLU* 1.3 65.0 + - + +
173B ASN* 3.3 2.9 + - - +
174B ARG* 3.1 22.1 + - - +
4E A 3.3 40.7 + - - +
5E C 3.4 34.7 + - - +
6E G 3.4 24.5 + - - -
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Residues in contact with GLU 171 (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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139B GLN* 5.1 9.0 - - + +
167B THR* 4.2 11.3 - - + +
168B PRO* 2.9 37.7 + - + +
170B LYS* 1.3 77.2 - - + +
172B ILE* 1.3 67.7 + - - +
174B ARG* 2.6 59.1 + - - +
175B VAL* 2.9 16.6 - - + +
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Residues in contact with ILE 172 (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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139B GLN* 4.9 3.4 - - + +
143B ILE* 3.9 20.6 - - + -
158B ALA* 3.7 21.5 - - + +
161B LEU* 3.9 11.4 - - + -
162B SER* 4.1 8.1 - - - -
165B LEU* 4.0 21.1 - - + -
167B THR* 4.0 29.4 - - + +
168B PRO 2.9 17.5 + - - +
169B LYS* 3.4 11.2 - - - +
171B GLU* 1.3 78.8 - - - +
173B ASN* 1.3 52.0 + - - +
175B VAL* 3.2 2.9 + - + +
176B LEU* 2.7 60.0 + - + +
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Residues in contact with ASN 173 (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 ALA* 3.2 21.7 - - - +
169B LYS* 2.8 24.8 + - - +
170B LYS 3.7 0.2 - - - +
171B GLU 3.2 0.2 - - - -
172B ILE* 1.3 74.4 - - - +
174B ARG* 1.3 57.3 + - - +
176B LEU* 3.9 6.9 - - - +
177B TYR* 2.7 58.5 + - + -
195B TRP* 4.5 1.9 + - - -
3E T 3.9 20.7 + - - -
4E A 2.7 47.6 + - - +
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Residues in contact with ARG 174 (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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139B GLN* 6.2 0.6 - - - +
170B LYS* 3.1 6.1 + - - +
171B GLU* 2.6 70.9 + - - +
173B ASN* 1.3 75.6 - - - +
175B VAL* 1.3 72.3 + - + +
177B TYR* 4.0 1.9 - - - +
178B SER* 3.0 25.6 + - - -
4E A 3.2 28.4 - - - +
5E C 3.4 22.3 + - - +
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Residues in contact with VAL 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B GLN* 3.9 21.8 - - + -
140B GLU* 3.6 37.5 - - + +
143B ILE* 3.3 23.8 - - + -
171B GLU* 2.9 23.9 + - + +
172B ILE* 3.4 6.1 - - + +
174B ARG* 1.3 84.7 - - + +
176B LEU* 1.3 57.0 + - - +
178B SER* 3.3 6.2 + - - -
179B LEU* 3.0 33.2 + - + +
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Residues in contact with LEU 176 (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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143B ILE* 3.6 24.9 - - + -
147B LEU* 4.9 1.6 - - + -
158B ALA* 3.7 14.1 - - + -
161B LEU* 5.0 5.8 - - + -
172B ILE* 2.7 46.4 + - + +
173B ASN* 3.5 7.0 - - - +
175B VAL* 1.3 70.7 - - - +
177B TYR* 1.3 65.2 + - - +
179B LEU* 3.3 3.5 + - - +
180B ALA 3.0 18.7 + - - -
185B LEU* 3.6 24.5 - - + +
195B TRP* 3.4 58.9 - - + +
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Residues in contact with TYR 177 (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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173B ASN* 2.7 39.9 + - - +
174B ARG* 4.2 2.5 - - - +
176B LEU* 1.3 72.9 - - - +
178B SER* 1.3 56.4 + - - +
180B ALA* 3.3 4.6 + - + +
181B LYS* 3.0 27.5 + - - +
187B LYS* 4.1 22.6 + - + -
193B PRO* 3.8 13.2 - - - +
195B TRP* 3.5 29.5 - + - -
2E G 4.0 2.9 + - - +
3E T 2.7 33.4 + - - -
4E A 3.6 45.7 + + + +
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Residues in contact with SER 178 (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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140B GLU* 4.5 7.7 + - - -
174B ARG 3.0 19.4 + - - -
175B VAL* 3.5 7.0 - - - -
176B LEU 3.1 0.2 - - - -
177B TYR* 1.3 73.7 - - - +
179B LEU* 1.3 66.1 + - - +
180B ALA 3.0 1.3 - - - -
181B LYS* 3.0 5.5 + - - +
182B LYS* 2.9 37.4 + - - +
181C LYS* 3.5 29.9 + - - +
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Residues in contact with LEU 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B GLU* 3.5 32.3 - - + +
143B ILE* 4.5 4.9 - - + -
144B LEU* 3.4 29.4 - - + -
175B VAL* 3.0 36.1 + - + +
176B LEU 3.3 0.6 + - - +
178B SER* 1.3 75.5 - - - +
180B ALA* 1.3 55.3 + - - +
182B LYS* 3.3 6.3 + - + -
183B GLY 2.9 6.4 + - - -
184B LYS* 2.7 65.2 + - + -
185B LEU* 3.5 27.8 - - + -
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Residues in contact with ALA 180 (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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176B LEU 3.0 16.7 + - - +
177B TYR* 3.5 7.9 - - + +
178B SER 3.0 0.2 - - - -
179B LEU* 1.3 75.8 - - - +
181B LYS* 1.3 61.1 + - - +
183B GLY* 3.0 16.8 + - - -
185B LEU* 4.0 17.2 - - + +
187B LYS* 4.5 10.3 - - + +
195B TRP* 3.6 22.2 - - + -
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Residues in contact with LYS 181 (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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177B TYR 3.0 13.2 + - - +
178B SER* 3.0 8.5 + - - +
180B ALA* 1.3 72.2 - - - +
182B LYS* 1.3 61.1 + - - +
183B GLY* 3.0 6.4 + - - -
174C ARG* 6.2 0.6 - - - +
178C SER* 2.9 39.1 + - - +
181C LYS* 3.9 26.7 - - + +
182C LYS* 3.2 56.0 + - + +
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Residues in contact with LYS 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B GLN* 5.6 3.2 - - - +
140B GLU* 3.3 24.5 + - - +
178B SER* 2.9 29.6 + - - +
179B LEU* 3.6 9.4 - - - +
180B ALA 3.2 0.2 - - - -
181B LYS* 1.3 75.4 - - - +
183B GLY* 1.3 61.4 + - - +
184B LYS* 3.5 26.8 + - + +
181C LYS* 3.2 35.3 - - + +
182C LYS* 5.0 5.8 - - - +
183C GLY* 5.9 0.3 - - - -
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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