Contacts of the helix formed by residues 175 - 183 (chain A) in PDB entry 3FZF
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 GLU 175 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A ASP* 4.1 5.8 - - - +
11A LEU 3.8 1.9 - - - +
71A LYS* 2.4 38.9 + - - -
145A THR* 3.5 23.6 - - - +
146A VAL* 2.6 25.7 + - - +
147A PRO* 3.4 15.2 - - + +
174A ASN* 1.3 69.4 - - - +
176A PRO* 1.4 65.5 - - + +
178A ALA* 3.2 6.4 + - - +
179A ALA* 3.0 23.4 + - - +
199A ASP* 5.0 10.8 - - - +
206A ASP* 5.8 0.2 - - - +
369A VAL* 3.8 28.9 - - + +
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Residues in contact with PRO 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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147A PRO* 5.2 0.2 - - + -
148A ALA* 4.0 19.7 - - + +
174A ASN* 3.5 9.0 - - + -
175A GLU* 1.4 95.4 - - + +
177A THR* 1.3 57.1 + - - +
179A ALA* 3.5 4.4 + - + +
180A ALA* 3.0 27.7 + - - +
197A ILE* 3.4 44.2 - - + +
208A SER* 3.8 26.9 - - - +
210A LEU* 4.2 8.1 - - + -
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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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173A ILE* 3.8 16.2 - - + -
174A ASN* 3.1 24.4 + - - +
176A PRO* 1.3 75.8 - - - +
178A ALA* 1.3 61.4 + - - +
180A ALA* 3.2 3.7 + - - +
181A ILE* 2.9 42.8 + - + +
210A LEU* 3.8 24.9 - - - +
217A PHE* 4.1 28.0 - - + +
219A VAL* 5.2 0.7 - - - +
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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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145A THR* 3.8 18.4 - - + -
173A ILE* 3.8 8.0 - - + +
174A ASN 3.0 11.8 + - - +
175A GLU 3.3 9.9 - - - +
177A THR* 1.3 76.4 - - - +
179A ALA* 1.3 56.3 + - - +
181A ILE* 3.2 7.8 + - - +
182A ALA* 3.0 23.6 + - - +
368A ALA 4.3 1.6 - - - -
369A VAL* 3.4 24.7 - - + +
372A GLY* 3.3 11.3 - - - -
373A ALA* 4.1 9.0 - - + +
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Residues in contact with ALA 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 GLU 3.0 13.1 + - - +
176A PRO* 3.7 11.9 - - + +
177A THR 3.3 0.2 - - - -
178A ALA* 1.3 75.5 - - - +
180A ALA* 1.3 59.9 + - - +
182A ALA* 3.5 7.0 + - - +
183A TYR* 3.3 25.5 - - - -
197A ILE* 4.5 2.5 - - + -
335A VAL* 4.1 8.7 - - + +
337A VAL* 3.7 30.7 - - + -
368A ALA* 4.1 13.7 + - + -
369A VAL* 4.5 7.1 - - + +
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Residues in contact with ALA 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 PRO 3.0 17.3 + - - +
177A THR 3.2 4.7 + - - +
179A ALA* 1.3 73.6 - - - +
181A ILE* 1.3 66.0 + - - +
183A TYR 3.4 5.2 + - - -
185A LEU* 3.1 47.2 + - + +
195A VAL* 4.9 4.5 - - + -
197A ILE* 5.2 1.1 - - + -
210A LEU* 4.4 6.7 - - + -
212A ILE* 4.3 7.0 - - + -
217A PHE* 3.7 22.4 - - + -
335A VAL* 4.9 3.1 - - - +
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Residues in contact with ILE 181 (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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173A ILE* 4.8 6.1 - - + -
177A THR* 2.9 36.7 + - + +
178A ALA* 3.5 10.5 - - - +
180A ALA* 1.3 74.0 - - - +
182A ALA* 1.3 58.2 + - - +
184A GLY* 2.8 21.8 + - - -
186A ASP* 3.9 26.0 - - - +
187A LYS* 5.8 0.5 - - - -
217A PHE* 3.9 15.7 - - + -
372A GLY* 3.4 24.0 - - - +
375A VAL* 4.0 21.2 - - + +
376A GLN* 4.0 28.9 - - + +
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Residues in contact with ALA 182 (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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178A ALA 3.0 6.8 + - - +
179A ALA* 3.6 11.2 - - - +
180A ALA 3.4 0.4 - - - -
181A ILE* 1.3 75.9 - - - +
183A TYR* 1.3 58.9 + - + +
184A GLY 3.4 2.1 + - - -
363A ILE* 3.3 28.5 - - + +
368A ALA* 3.7 25.1 - - - +
371A TYR* 3.7 27.0 + - + -
372A GLY* 3.7 8.3 - - - +
375A VAL* 5.3 1.3 - - - +
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Residues in contact with TYR 183 (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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179A ALA 3.3 20.8 + - - -
180A ALA 3.4 2.5 + - - +
181A ILE 3.2 0.8 - - - -
182A ALA* 1.3 74.9 - - - +
184A GLY* 1.3 63.7 + - - +
185A LEU* 3.1 28.3 + - + +
188A LYS* 5.8 0.2 - - - -
335A VAL* 3.6 26.5 - - + -
336A LEU 4.5 3.6 + - - -
360A ASN* 3.5 27.4 - - + +
361A LYS* 2.9 20.7 - - - -
362A SER* 2.8 33.2 + - - -
363A ILE* 3.0 36.9 + - + +
368A ALA* 4.8 8.5 - - + +
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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