Contacts of the helix formed by residues 165 - 173 (chain B) in PDB entry 2F37
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 165 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121B MSE 4.2 3.6 - - - -
152B VAL 5.1 4.3 - - - -
153B ASN* 5.2 4.3 - - - -
154B ALA 3.8 15.7 - - - -
155B GLN* 4.1 6.5 - - - -
163B GLY 4.0 5.4 - - - -
164B HIS* 1.3 75.9 - - - +
166B ALA* 1.3 65.4 + - - +
167B LEU* 3.4 15.7 + - - +
168B HIS* 2.8 40.3 + - - +
169B ILE* 3.1 17.1 + - - +
188B ASN 5.1 0.5 + - - -
191B ALA* 4.4 9.0 - - - +
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Residues in contact with ALA 166 (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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120B LEU* 3.8 35.0 - - + -
121B MSE 4.1 21.2 - - + +
124B VAL* 4.0 8.7 - - + +
152B VAL 4.3 8.2 + - - +
154B ALA 4.5 1.4 + - - -
165B SER* 1.3 74.4 - - - +
167B LEU* 1.3 62.7 + - - +
169B ILE* 3.1 9.0 + - - +
170B ALA 3.0 19.2 + - - -
182B LEU* 3.6 16.9 - - + +
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Residues in contact with LEU 167 (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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152B VAL 5.2 1.6 + - - +
165B SER* 3.1 10.1 + - - +
166B ALA* 1.3 79.3 - - - +
168B HIS* 1.3 62.1 + - - +
170B ALA* 3.3 1.6 + - - +
171B ILE* 3.0 39.4 + - + +
179B VAL* 3.9 36.1 - - + +
182B LEU* 3.9 12.8 - - + +
183B VAL* 3.9 10.1 - - + -
187B ALA* 4.3 17.5 - - + -
188B ASN 3.7 24.2 - - - +
189B VAL* 3.8 25.8 - - + -
212B PRO* 3.8 13.7 - - + -
228B LEU* 4.8 2.0 - - + -
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Residues in contact with HIS 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B GLY 3.9 7.0 - - - -
164B HIS* 3.5 22.3 - - + -
165B SER* 2.8 37.7 + - - +
167B LEU* 1.3 76.9 - - - +
169B ILE* 1.3 63.5 + - - +
171B ILE* 3.3 2.7 + - - -
172B GLU* 2.9 21.8 + - - +
191B ALA* 3.2 27.6 + - + -
193B ALA* 3.6 19.4 + - + -
208B PHE* 4.0 14.6 - + - -
210B GLU 2.9 25.8 + - - -
212B PRO* 3.5 18.3 - - + +
215B LEU* 3.4 18.7 - - + +
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Residues in contact with ILE 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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117B LYS* 5.9 0.7 - - + +
121B MSE 3.8 38.1 - - + +
124B VAL* 3.7 18.2 - - + -
125B LEU* 3.7 43.1 - - + +
164B HIS* 3.5 29.6 - - + +
165B SER 3.1 8.3 + - - +
166B ALA* 3.1 8.6 + - - +
168B HIS* 1.3 77.4 - - - +
170B ALA* 1.3 56.5 + - - +
172B GLU* 3.1 8.3 + - + +
173B LYS* 2.9 35.8 + - + +
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Residues in contact with ALA 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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124B VAL* 3.5 14.2 - - + +
127B LEU* 5.1 0.7 - - - -
166B ALA 3.0 6.4 + - - +
167B LEU 3.3 8.3 + - - +
169B ILE* 1.3 75.1 - - - +
171B ILE* 1.3 62.5 + - - +
173B LYS* 3.4 4.8 + - - +
174B ARG 3.2 3.5 + - - -
175B SER* 3.2 24.8 + - - +
178B CYS* 3.9 14.6 - - + -
179B VAL* 3.9 15.9 - - + +
182B LEU* 3.6 27.1 - - + -
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Residues in contact with ILE 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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167B LEU* 3.0 25.5 + - + +
168B HIS* 3.7 4.3 - - - +
170B ALA* 1.3 76.7 - - - +
172B GLU* 1.3 57.8 + - - +
174B ARG* 2.8 15.0 + - - +
179B VAL* 3.6 20.2 - - + -
212B PRO* 3.5 42.4 - - + +
215B LEU* 3.7 22.4 - - + -
216B ALA* 3.8 16.8 - - + -
221B GLN* 2.8 37.1 + - - +
224B VAL* 4.0 7.6 - - + -
228B LEU* 4.0 11.4 - - + -
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Residues in contact with GLU 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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164B HIS* 4.5 16.6 + - - -
168B HIS 2.9 15.6 + - - +
169B ILE* 3.1 7.1 + - + +
171B ILE* 1.3 76.7 - - - +
173B LYS* 1.3 63.6 + - + +
174B ARG* 3.3 11.6 + - - +
206B PHE* 3.5 38.3 - - + -
215B LEU* 4.1 12.0 - - + +
219B THR* 5.8 4.3 - - + -
221B GLN* 4.8 2.2 - - - +
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Residues in contact with LYS 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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124B VAL 3.3 22.9 - - - +
125B LEU* 3.0 29.6 + - + +
127B LEU* 3.6 38.9 + - + -
130B GLY* 6.1 0.3 - - - -
169B ILE* 2.9 25.8 + - + +
170B ALA 3.7 5.4 - - - +
171B ILE 3.2 0.4 - - - -
172B GLU* 1.3 74.5 - - + +
174B ARG* 1.3 70.7 + - - +
175B SER* 3.4 2.1 + - - -
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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