Contacts of the helix formed by residues 170 - 180 (chain A) in PDB entry 4FGB
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 ASP 170 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166A SER 3.9 2.9 - - - +
167A LYS* 3.4 54.8 + - + +
168A MET 3.1 0.4 - - - -
169A GLU* 1.3 78.4 - - - +
171A PRO* 1.4 69.4 - - + +
172A GLY* 3.1 2.9 - - - +
173A SER* 2.8 25.4 + - - +
174A VAL 2.9 9.4 + - - -
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Residues in contact with PRO 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A GLU 3.4 4.2 - - - +
170A ASP* 1.4 86.9 - - + +
172A GLY* 1.3 60.8 + - - +
173A SER 3.3 0.2 - - - -
174A VAL* 3.5 6.8 - - + +
175A LEU* 3.1 32.0 + - + +
192A GLN* 3.7 27.1 - - - +
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Residues in contact with GLY 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A PHE* 6.1 3.1 - - - -
170A ASP* 3.0 2.2 + - - +
171A PRO* 1.3 81.4 - - - +
173A SER* 1.3 57.1 + - - +
175A LEU* 3.4 9.0 + - - +
176A SER* 3.1 26.9 + - - -
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Residues in contact with SER 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ALA* 3.7 27.3 - - - +
31A PHE* 4.2 13.0 - - - -
167A LYS* 2.8 27.6 + - - +
168A MET* 3.5 14.6 - - - -
170A ASP* 2.8 12.8 + - - +
172A GLY* 1.3 73.4 - - - +
174A VAL* 1.3 53.9 + - - +
176A SER* 3.2 4.5 + - - -
177A THR* 2.6 41.6 + - - -
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Residues in contact with VAL 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A MET 3.4 13.7 - - - +
169A GLU 3.4 14.4 - - - +
170A ASP 2.9 17.7 + - - +
171A PRO* 3.5 6.1 - - + +
173A SER* 1.3 76.3 - - - +
175A LEU* 1.3 58.0 + - + +
177A THR* 3.2 10.3 + - - -
178A ALA* 2.9 24.4 + - + +
189A VAL* 3.1 36.5 - - + +
190A LEU* 5.1 2.8 - - - +
192A GLN* 3.2 28.5 - - + +
193A LYS 5.9 2.2 - - - +
195A TYR* 4.2 11.2 - - + -
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Residues in contact with LEU 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A PRO* 3.1 23.9 + - + +
172A GLY* 3.9 5.6 - - - +
174A VAL* 1.3 74.8 - - + +
176A SER* 1.3 60.0 - - - +
178A ALA* 3.3 11.6 + - + +
179A CYS* 2.9 38.6 + - - -
190A LEU 5.9 1.8 - - - +
192A GLN* 3.7 30.1 - - + +
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Residues in contact with SER 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A GLY 5.3 1.6 + - - -
30A ALA* 4.7 15.8 - - - -
172A GLY 3.1 15.2 + - - -
173A SER* 3.4 12.6 - - - -
175A LEU* 1.3 75.1 - - - +
177A THR* 1.3 64.1 + - - -
179A CYS* 3.2 6.6 + - - +
180A GLY* 3.0 21.1 + - - -
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Residues in contact with THR 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ALA* 5.7 1.2 - - - +
140A ARG 5.4 3.4 - - - +
141A ASP* 5.3 8.7 - - - +
168A MET* 4.2 12.7 - - - +
173A SER 2.6 28.1 + - - -
174A VAL* 3.2 11.4 + - - -
176A SER* 1.3 73.3 - - - +
178A ALA* 1.3 63.6 + - - +
180A GLY* 3.3 12.6 + - - -
181A THR 3.9 6.5 + - - +
185A VAL* 3.8 36.5 - - + +
189A VAL* 5.3 0.4 - - - -
195A TYR* 4.0 18.2 + - - +
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Residues in contact with ALA 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A VAL* 2.9 14.9 + - + +
175A LEU* 3.3 20.6 - - + +
177A THR* 1.3 77.3 - - - +
179A CYS* 1.3 59.0 + - - +
182A PRO* 3.0 29.2 - - - +
190A LEU* 3.7 30.5 - - + +
227A PHE* 3.3 15.9 - - + -
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Residues in contact with CYS 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A LEU* 2.9 29.5 + - - +
176A SER* 3.2 7.8 + - - +
178A ALA* 1.3 78.1 - - - +
180A GLY* 1.3 67.2 + - - +
182A PRO* 4.7 2.2 - - - +
227A PHE* 5.1 3.6 - - - -
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Residues in contact with GLY 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A SER 3.0 13.6 + - - -
177A THR* 3.3 4.4 + - - -
179A CYS* 1.3 83.2 - - - +
181A THR* 1.3 64.7 + - - +
182A PRO* 3.4 5.7 - - - +
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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