Contacts of the helix formed by residues 162 - 171 (chain B) in PDB entry 1CF5
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 PHE 162 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B ARG* 3.9 0.7 - - - -
158B GLU* 3.1 15.2 + - - -
159B ALA 3.1 8.6 + - - +
161B ARG* 1.3 87.7 - - + +
163B LYS* 1.3 65.9 + - - +
165B ILE* 3.1 32.9 + - + +
166B GLU 3.0 15.8 + - - -
186B LEU* 3.4 46.0 - - + -
187B GLU 4.3 0.2 - - - -
190B TRP* 3.5 33.9 - + + -
193B LEU* 3.9 17.5 - - + -
234B ASN* 3.6 15.7 - - - +
235B ILE* 3.9 31.0 - - + -
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Residues in contact with LYS 163 (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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22B ARG* 3.8 10.2 - - - +
162B PHE* 1.3 70.5 - - - +
164B TYR* 1.3 65.8 + - - +
166B GLU* 2.7 23.7 + - - +
167B ARG* 2.7 62.1 + - + +
233B GLY* 3.9 17.9 + - - +
234B ASN 2.8 18.8 + - - +
236B LYS* 3.4 30.5 - - - +
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Residues in contact with TYR 164 (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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163B LYS* 1.3 73.2 - - - +
165B ILE* 1.3 58.8 + - + +
167B ARG* 3.4 5.3 + - - +
168B HIS* 2.8 67.6 + + - -
180B ASN* 3.1 18.2 + - - -
182B ALA* 4.1 10.5 - - + -
183B ILE* 3.8 26.7 - - + -
186B LEU* 3.9 20.0 - - + -
216B PRO* 3.7 15.2 - - + +
234B ASN* 2.8 33.0 - - - +
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Residues in contact with ILE 165 (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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125B LEU* 5.9 3.1 - - + -
154B GLN* 4.0 22.4 - - + +
158B GLU* 4.0 11.0 - - + +
159B ALA* 4.2 5.6 - - + +
162B PHE* 3.1 39.8 + - + +
164B TYR* 1.3 77.8 - - + +
166B GLU* 1.3 65.4 + - - +
167B ARG 3.1 1.9 + - - -
168B HIS* 3.3 6.3 + - + +
169B VAL* 2.9 28.5 + - + +
177B PHE* 6.1 1.8 - - + -
183B ILE* 4.1 47.1 - - + +
186B LEU* 4.2 5.8 - - + -
187B GLU* 4.3 12.3 - - + +
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Residues in contact with GLU 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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14B TYR* 3.3 10.7 - - + -
15B THR* 3.4 29.8 - - + +
18B ILE* 3.9 19.3 - - + -
22B ARG* 2.9 32.5 + - - +
159B ALA* 3.7 30.2 - - + +
162B PHE 3.0 6.1 + - - +
163B LYS* 2.7 32.3 + - - +
165B ILE* 1.3 73.6 - - - +
167B ARG* 1.3 60.0 + - - +
169B VAL* 4.0 1.1 - - - -
170B ALA* 3.2 21.3 + - - +
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Residues in contact with ARG 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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15B THR* 6.3 1.3 - - + -
163B LYS* 2.7 53.2 + - + +
164B TYR* 3.7 6.5 - - - +
166B GLU* 1.3 76.9 - - - +
168B HIS* 1.3 69.3 + - + +
170B ALA* 2.9 21.7 + - + +
171B LYS* 3.2 10.5 + - - +
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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
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164B TYR* 2.8 74.2 + + - +
165B ILE 3.3 4.7 + - - +
167B ARG* 1.3 78.6 - - + +
169B VAL* 1.3 61.3 + - - +
171B LYS* 3.3 10.8 + - - +
172B TYR* 3.1 29.4 + - + -
177B PHE* 4.0 13.4 - - + -
180B ASN* 3.2 18.5 + - - -
183B ILE* 3.8 22.7 - - + +
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Residues in contact with VAL 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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14B TYR* 3.1 40.8 - - + +
126B GLY 4.3 13.5 - - - -
127B LEU* 3.8 20.5 - - + +
155B THR* 4.3 19.5 - - + -
159B ALA* 4.6 2.9 - - + -
165B ILE* 2.9 23.6 - - + +
166B GLU 3.5 0.7 - - - +
168B HIS* 1.3 77.0 - - - +
170B ALA* 1.3 62.8 + - - +
171B LYS 3.1 1.4 + - - -
172B TYR 3.3 16.8 + - - +
177B PHE* 3.6 20.4 - - + -
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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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11B ALA* 2.9 20.6 - - + +
14B TYR* 3.6 11.4 - - + -
15B THR* 3.7 25.4 - - + -
127B LEU* 5.4 0.2 - - - -
166B GLU 3.2 16.3 + - - +
167B ARG* 2.9 15.9 + - + +
169B VAL* 1.3 79.4 - - - +
171B LYS* 1.3 50.8 + - - +
173B VAL* 2.9 27.8 - - - +
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Residues in contact with LYS 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 ARG 3.2 10.3 + - - +
168B HIS* 3.4 13.2 - - - +
169B VAL 3.1 0.2 - - - -
170B ALA* 1.3 74.7 - - - +
172B TYR* 1.3 90.9 + - + +
173B VAL* 3.1 15.3 + - - +
175B THR* 5.1 1.4 - - - +
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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