Contacts of the helix formed by residues 159 - 170 (chain C) in PDB entry 3F7G
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 159 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154C LEU 3.8 0.2 + - - -
155C LEU* 2.8 30.2 + - - -
156C ARG 4.6 0.6 + - - -
157C SER 3.8 0.6 - - - -
158C LYS* 1.3 77.6 - - - +
160C ARG* 1.3 64.2 + - - -
161C ASP 3.4 2.7 - - - -
162C PHE* 3.6 0.7 + - - +
163C VAL* 3.4 23.2 + - - +
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Residues in contact with ARG 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C LEU* 3.8 40.7 + - + +
159C GLY* 1.3 70.3 - - - -
161C ASP* 1.3 65.4 + - - +
163C VAL* 3.3 2.0 + - + +
164C HIS* 2.9 34.7 + - + +
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Residues in contact with ASP 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159C GLY 3.4 0.8 - - - -
160C ARG* 1.3 81.8 - - - +
162C PHE* 1.3 56.4 + - - +
164C HIS* 3.7 7.4 + - - +
165C SER* 3.0 30.3 + - - -
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Residues in contact with PHE 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C TRP* 3.9 17.9 - - + -
142C THR* 4.1 21.8 - - - -
145C ALA* 3.9 21.3 - - + -
154C LEU* 4.6 1.6 - - + -
158C LYS* 3.4 47.7 + - + +
159C GLY 3.6 1.9 + - - +
160C ARG 3.3 0.4 - - - -
161C ASP* 1.3 78.7 - - - +
163C VAL* 1.3 69.2 + - + +
165C SER* 3.3 7.3 + - - -
166C VAL* 3.0 41.0 + - + +
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Residues in contact with VAL 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C ALA* 4.1 17.3 - - + +
149C PRO* 3.4 42.2 - - + +
154C LEU* 3.8 28.0 - - + +
155C LEU* 3.7 17.7 - - + -
159C GLY 3.4 14.5 + - - +
160C ARG* 3.3 6.6 + - + +
162C PHE* 1.3 79.2 - - + +
164C HIS* 1.3 58.7 + - - +
166C VAL* 3.3 2.3 + - - +
167C GLN* 2.9 30.5 + - + +
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Residues in contact with HIS 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C ARG* 2.9 21.2 + - + +
161C ASP* 3.7 6.7 + - - +
163C VAL* 1.3 78.2 - - - +
165C SER* 1.3 62.9 + - - +
167C GLN* 3.3 8.4 + - + +
168C GLU* 3.0 52.8 + - + +
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Residues in contact with SER 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161C ASP 3.0 19.0 + - - -
162C PHE* 3.5 8.1 - - - -
164C HIS* 1.3 79.1 + - - +
166C VAL* 1.3 62.5 + - - +
168C GLU* 3.2 17.6 + - - +
169C THR* 3.1 37.8 + - - +
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Residues in contact with VAL 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C THR* 3.5 35.0 - - + +
145C ALA* 3.8 5.8 - - + -
146C LYS* 3.6 22.2 - - + +
162C PHE* 3.0 46.3 + - + +
163C VAL 3.7 3.8 - - - +
165C SER* 1.3 73.5 - - - +
167C GLN* 1.3 61.5 + - - +
169C THR* 3.3 1.3 + - - -
170C HIS* 2.8 54.8 + - + +
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Residues in contact with GLN 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B PRO* 4.9 5.1 - - - +
167B GLN* 4.4 16.7 - - - +
145C ALA 2.9 15.7 - - - +
146C LYS* 2.9 28.7 + - - +
149C PRO* 3.6 28.6 - - + +
163C VAL* 2.9 22.3 + - + +
164C HIS* 3.6 9.2 - - + +
166C VAL* 1.3 77.9 - - - +
168C GLU* 1.3 57.8 + - - +
170C HIS 3.5 6.1 - - - +
171C SER* 2.9 30.4 - - - -
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Residues in contact with GLU 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C HIS* 3.0 39.9 + - + +
165C SER* 3.2 29.2 + - - +
167C GLN* 1.3 77.5 - - - +
169C THR* 1.3 68.0 + - + +
170C HIS 3.4 0.4 + - - -
171C SER* 4.1 11.5 + - - -
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Residues in contact with THR 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C SER* 3.1 24.6 + - - +
166C VAL* 3.9 1.0 - - - -
168C GLU* 1.3 85.8 - - + +
170C HIS* 1.3 87.4 + - - +
171C SER 3.6 1.8 + - - -
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Residues in contact with HIS 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B ALA* 6.2 4.0 - - + -
142C THR* 4.0 24.9 - - + +
143C GLU* 6.1 1.1 - - - -
146C LYS* 4.0 41.7 - - + +
166C VAL* 2.8 29.4 + - + +
167C GLN* 3.5 7.2 - - - +
169C THR* 1.3 104.3 + - - +
171C SER* 1.3 61.0 + - - +
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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