Contacts of the helix formed by residues 168 - 180 (chain F) in PDB entry 3CB4
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 GLY 168 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535D HIS* 3.6 16.5 + - - +
159F VAL* 4.0 2.6 - - - +
160F ARG 3.8 11.4 - - - +
161F CYS* 3.9 4.9 - - - -
166F GLY 3.6 0.8 + - - -
167F VAL* 1.3 72.0 - - - +
169F VAL* 1.3 59.7 + - - +
170F GLN* 3.2 3.4 - - - +
171F ASP* 3.2 25.3 + - - +
172F VAL* 3.0 29.3 + - - +
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Residues in contact with VAL 169 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F LEU* 3.9 25.8 - - + -
23F ARG* 4.1 13.2 - - + +
24F ILE* 4.1 28.3 - - + +
27F ILE* 3.9 13.7 - - + -
161F CYS* 3.9 16.8 - - + -
162F SER 4.3 4.5 - - - +
166F GLY* 3.4 30.2 + - - +
167F VAL 3.2 0.4 - - - -
168F GLY* 1.3 74.8 - - - +
170F GLN* 1.3 64.0 + - - +
172F VAL* 3.3 10.8 - - - +
173F LEU* 3.2 21.1 + - - +
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Residues in contact with GLN 170 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534D THR 4.4 3.1 - - - +
535D HIS* 4.2 10.5 - - + -
536D ILE* 3.3 60.3 + - + +
539D ARG* 4.4 2.4 - - - +
27F ILE* 3.6 19.0 - - + +
63F TYR* 3.3 35.4 + - + +
64F LYS 5.2 0.6 + - - -
66F SER* 6.0 0.8 - - - +
166F GLY 4.6 1.6 + - - -
168F GLY 3.2 1.3 - - - +
169F VAL* 1.3 77.6 - - - +
171F ASP* 1.3 62.7 + - - +
173F LEU* 3.0 6.3 + - - +
174F GLU* 2.8 30.7 + - + +
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Residues in contact with ASP 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535D HIS* 2.8 37.0 + - - -
159F VAL* 3.6 17.9 - - + +
168F GLY* 3.2 15.2 + - - +
170F GLN* 1.3 78.6 - - - +
172F VAL* 1.3 59.2 + - - +
174F GLU* 3.5 14.0 - - - +
175F ARG* 2.9 29.6 + - - +
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Residues in contact with VAL 172 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F LEU* 4.2 18.2 - - + -
99F LEU* 4.2 15.3 - - + +
127F VAL* 5.4 1.6 - - + +
129F VAL* 3.8 41.1 - - + -
159F VAL* 4.1 16.8 - - + +
161F CYS* 4.2 9.4 - - - -
168F GLY 3.0 20.4 + - - +
169F VAL* 3.3 15.0 - - + +
170F GLN 3.2 0.4 - - - -
171F ASP* 1.3 77.0 - - - +
173F LEU* 1.3 62.7 + - + +
175F ARG* 3.5 4.7 + - - +
176F LEU* 3.0 27.1 + - + +
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Residues in contact with LEU 173 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F ILE* 3.7 34.1 - - + -
27F ILE* 3.5 17.0 - - + -
28F CYS* 3.5 32.5 - - - -
63F TYR* 3.7 26.2 - - + -
73F LEU* 3.9 15.7 - - + -
169F VAL 3.2 15.7 + - - +
170F GLN 3.0 9.9 + - - +
172F VAL* 1.3 82.0 - - + +
174F GLU* 1.3 64.1 + - - +
176F LEU* 3.3 12.6 - - + +
177F VAL* 3.2 28.6 + - - +
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Residues in contact with GLU 174 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63F TYR* 2.7 35.0 + - - +
65F ALA* 3.5 4.7 - - - +
66F SER* 2.7 47.5 + - - -
170F GLN* 2.8 18.0 + - + +
171F ASP* 3.5 18.8 - - - +
173F LEU* 1.3 76.2 - - - +
175F ARG* 1.3 62.6 + - - +
177F VAL* 3.5 5.1 + - - +
178F ARG* 3.1 22.7 + - - +
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Residues in contact with ARG 175 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127F VAL* 3.8 24.7 - - + -
128F PRO* 6.4 0.2 - - - +
157F ASP* 2.6 52.8 + - - +
158F ALA* 4.8 0.6 - - - +
159F VAL* 3.5 25.5 - - + +
171F ASP 2.9 16.9 + - - +
172F VAL 3.7 4.9 - - - +
174F GLU* 1.3 72.4 - - - +
176F LEU* 1.3 68.1 + - - +
178F ARG* 3.0 47.4 + - - +
179F ASP* 3.0 38.6 + - - +
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Residues in contact with LEU 176 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F ARG* 3.8 20.9 - - + -
7F PHE* 3.4 52.5 - - + -
24F ILE* 5.7 0.2 - - + -
73F LEU* 4.2 9.0 - - + -
99F LEU* 4.1 16.8 - - + -
127F VAL* 4.7 7.6 - - - +
172F VAL 3.0 14.8 + - - +
173F LEU* 3.3 26.9 - - + +
175F ARG* 1.3 75.4 - - - +
177F VAL* 1.3 58.3 + - - +
180F ILE* 2.9 56.2 + - + +
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Residues in contact with VAL 177 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F ARG* 2.9 40.9 + - + +
63F TYR* 4.6 10.5 - - + -
65F ALA* 5.1 4.3 - - + -
67F ASP* 5.7 0.2 - - - +
71F TYR* 3.6 57.0 - - + +
73F LEU* 4.1 21.1 - - + -
173F LEU 3.2 16.0 + - - +
174F GLU* 3.8 5.8 - - - +
176F LEU* 1.3 79.6 - - + +
178F ARG* 1.3 62.4 + - - +
179F ASP 3.6 0.2 + - - -
180F ILE 3.7 1.7 - - - +
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Residues in contact with ARG 178 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157F ASP* 4.5 8.1 + - - +
174F GLU 3.1 12.8 + - - +
175F ARG* 3.0 49.2 + - - +
177F VAL* 1.3 79.7 - - - +
179F ASP* 1.3 87.5 + - - +
180F ILE 5.0 0.3 - - - +
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Residues in contact with ASP 179 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125F GLU* 3.4 33.6 - - - +
127F VAL* 4.7 12.1 - - + +
175F ARG* 3.0 21.6 + - - +
178F ARG* 1.3 123.7 + - - +
180F ILE* 1.3 63.4 + - - +
181F PRO* 3.5 2.8 - - - +
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Residues in contact with ILE 180 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F ARG* 2.9 41.8 + - + -
6F ASN 4.0 7.9 - - - +
7F PHE* 3.8 26.5 - - + -
96F GLU* 3.9 2.9 - - + -
97F GLY* 3.8 33.4 - - - +
98F ALA 4.0 4.9 - - - +
99F LEU* 5.0 1.1 - - + -
125F GLU* 4.0 11.7 - - + +
127F VAL* 4.3 14.8 - - + -
176F LEU* 2.9 32.5 + - + +
177F VAL 3.7 2.6 - - - +
178F ARG 4.9 0.6 - - - -
179F ASP* 1.3 76.6 - - - +
181F PRO* 1.3 76.4 - - + +
182F PRO* 4.1 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