Contacts of the helix formed by residues 171 - 179 (chain A) in PDB entry 4UC5
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 SER 171 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A THR* 3.1 16.0 + - - +
170A GLU* 1.3 75.6 - - - +
172A GLN* 1.3 65.1 + - - +
173A VAL* 3.4 13.0 - - - +
174A HIS* 2.8 35.3 + - - +
175A ARG* 3.2 24.4 + - - +
167B ARG 3.4 12.8 + - - -
168B THR* 3.7 20.5 - - - +
171B SER* 4.9 2.2 - - - -
174B HIS* 4.8 0.2 - - - -
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Residues in contact with GLN 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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170A GLU 3.5 3.2 + - - -
171A SER* 1.3 74.0 + - - +
173A VAL* 1.3 65.8 + - - +
175A ARG* 3.1 8.2 + - + +
176A GLU* 2.9 44.1 + - + +
209A HIS* 6.1 1.3 - - + -
98B GLU* 3.0 27.5 + - - +
100B PRO* 3.5 20.6 - - + +
101B ARG 3.0 25.3 + - - +
107B LYS* 2.8 27.4 + - - +
147B LEU* 4.5 11.2 - - + +
167B ARG* 3.4 19.5 - - - +
168B THR* 4.8 4.2 - - - +
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Residues in contact with VAL 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A MET* 3.7 40.1 - - + +
171A SER* 3.4 12.8 - - - +
172A GLN* 1.3 81.2 - - - +
174A HIS* 1.3 58.3 + - - +
176A GLU* 3.2 17.9 + - - +
177A LEU* 2.8 26.5 + - - +
211A PHE* 4.4 10.0 - - + +
212A LEU 5.7 1.3 - - - +
147B LEU* 3.7 24.2 - - + +
148B ASP* 4.4 14.8 - - + +
149B MET* 4.9 0.7 - - + -
168B THR* 5.5 0.6 - - + +
174B HIS* 3.8 9.9 - - + -
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Residues in contact with HIS 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A PHE 4.1 14.4 - - - -
147A LEU 2.9 26.7 + - - -
148A ASP 4.7 0.2 - - - -
149A MET* 4.1 13.3 - - + +
164A ILE* 4.3 17.0 - - + +
168A THR* 3.6 45.6 - - + +
171A SER* 2.8 24.4 + - - +
172A GLN 3.2 0.8 - - - -
173A VAL* 1.3 79.9 - - + +
175A ARG* 1.3 61.0 + - - +
177A LEU* 3.4 11.6 - - + +
178A ALA* 3.0 26.7 + - - +
187A PHE* 5.2 0.4 - - - -
171B SER* 3.7 13.5 - - - -
173B VAL* 3.8 11.2 - - + +
174B HIS* 4.0 6.5 - + - -
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Residues in contact with ARG 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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169A THR 2.8 23.5 + - - +
170A GLU* 3.7 16.5 - - - +
171A SER 3.2 14.9 + - - +
172A GLN* 3.1 9.3 + - + +
174A HIS* 1.3 75.8 - - - +
176A GLU* 1.3 59.4 + - + +
178A ALA* 3.3 8.6 + - - +
179A SER* 3.0 26.9 + - - -
187A PHE* 4.4 6.5 - - + -
197A ILE* 2.8 34.4 + - - +
200A ASP* 3.7 12.5 + - - +
201A ALA* 3.7 25.1 - - + +
204A ALA* 4.4 17.2 - - + +
205A ALA* 3.8 6.7 - - - +
209A HIS* 5.3 2.0 - - - +
101B ARG 6.0 0.2 - - - -
102B THR* 3.3 30.9 + - - +
167B ARG* 3.4 25.7 - - - +
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Residues in contact with GLU 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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172A GLN* 2.9 43.4 + - + +
173A VAL* 3.4 22.1 + - - +
175A ARG* 1.3 75.4 - - + +
177A LEU* 1.3 64.8 + - - +
179A SER* 2.5 25.9 + - - -
180A GLY 3.6 1.7 + - - -
209A HIS* 3.8 30.3 + - + +
210A HIS 3.4 18.9 + - - +
211A PHE* 3.6 25.8 - - + +
98B GLU* 4.6 1.9 - - - +
107B LYS* 4.1 14.6 + - - +
111B ASN* 5.7 1.4 + - - -
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Residues in contact with LEU 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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146A PHE* 3.9 26.5 - - + +
148A ASP 3.6 21.5 - - - +
149A MET* 4.1 17.5 - - + +
152A PRO* 4.1 19.1 - - + -
164A ILE* 4.8 5.4 - - + -
173A VAL 2.8 13.4 + - - +
174A HIS* 3.4 14.1 - - + +
176A GLU* 1.3 75.5 - - - +
178A ALA* 1.3 58.1 + - - +
180A GLY* 2.8 21.4 + - - -
181A LEU* 3.2 25.7 + - + +
211A PHE* 3.8 30.9 - - + -
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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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164A ILE* 4.5 3.8 - - + -
174A HIS 3.0 11.0 + - - +
175A ARG 3.3 9.8 + - - +
177A LEU* 1.3 76.1 - - - +
179A SER* 1.3 62.1 + - - +
180A GLY 3.0 1.6 + - - -
181A LEU* 3.3 16.5 + - - +
185A VAL* 4.2 13.7 - - + -
187A PHE* 3.5 32.3 - - + -
205A ALA* 4.0 4.5 - - + -
228A ASN* 3.1 26.9 + - - +
231A CYS* 5.1 0.2 - - - -
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Residues in contact with SER 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ARG 3.0 12.1 + - - -
176A GLU 2.5 21.5 + - - -
178A ALA* 1.3 77.1 - - - +
180A GLY* 1.3 52.9 + - - +
181A LEU 3.7 0.2 - - - -
205A ALA 3.2 25.1 + - - -
207A HIS 3.3 16.6 - - - -
209A HIS* 3.6 12.8 - - - +
225A THR* 2.8 21.7 + - - +
227A GLY 3.2 29.6 + - - +
228A ASN* 4.0 3.0 - - - +
11B LYS* 4.1 2.4 - - - +
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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