Contacts of the helix formed by residues 171 - 180 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168C THR* 2.9 20.7 + - - +
170C GLU* 1.3 78.3 - - - +
172C GLN* 1.3 63.7 + - - +
173C VAL* 3.5 9.5 - - - +
174C HIS* 2.7 33.2 + - - -
175C ARG* 3.2 22.2 + - - +
167D ARG* 3.9 12.0 + - - -
168D THR* 3.9 21.5 - - - +
171D SER* 5.0 2.7 - - - -
174D HIS* 4.7 0.4 - - - -
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Residues in contact with GLN 172 (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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170C GLU 3.4 3.6 + - - -
171C SER* 1.3 71.8 + - - +
173C VAL* 1.3 57.9 + - - +
175C ARG* 3.1 8.5 + - + +
176C GLU* 3.0 44.6 + - + +
209C HIS* 6.2 1.6 - - + +
98D GLU* 3.1 27.7 + - - -
100D PRO* 3.5 24.2 - - + +
101D ARG 3.1 24.7 + - - +
107D LYS* 2.7 27.0 + - - +
147D LEU* 4.8 8.0 - - + +
167D ARG* 3.4 23.9 - - - +
168D THR* 4.9 4.2 - - - +
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Residues in contact with VAL 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C MET* 3.8 38.6 - - + -
171C SER* 3.5 11.7 - - - +
172C GLN* 1.3 79.6 - - - +
174C HIS* 1.3 63.3 + - - +
176C GLU* 3.2 17.6 + - - +
177C LEU* 2.8 27.0 + - - +
211C PHE* 4.2 11.4 - - + -
212C LEU 5.6 1.6 - - - +
147D LEU* 3.7 25.1 - - + +
148D ASP* 4.5 14.8 - - + +
168D THR* 5.5 0.4 - - + -
174D HIS* 3.9 7.2 - - + -
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Residues in contact with HIS 174 (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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146C PHE 4.1 15.0 - - - -
147C LEU 3.0 25.7 + - - -
148C ASP 4.7 0.2 - - - -
149C MET* 4.1 17.6 - - + +
164C ILE* 4.2 16.8 - - + +
168C THR* 3.7 45.8 - - + +
171C SER* 2.7 25.1 + - - +
172C GLN 3.2 0.4 - - - -
173C VAL* 1.3 77.8 - - - +
175C ARG* 1.3 62.3 + - - +
177C LEU* 3.3 10.3 - - + +
178C ALA* 3.1 22.0 + - - +
187C PHE* 5.2 1.6 - - - -
171D SER* 3.9 5.2 - - - -
173D VAL* 3.9 20.6 - - + +
174D HIS* 4.1 6.5 - + - -
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Residues in contact with ARG 175 (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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169C THR 2.9 23.5 + - - +
170C GLU* 3.8 15.0 + - - +
171C SER 3.2 14.6 + - - +
172C GLN* 3.1 9.5 + - + +
174C HIS* 1.3 75.8 - - - +
176C GLU* 1.3 64.8 + - + +
178C ALA* 3.2 8.3 + - - +
179C SER* 3.1 21.1 + - - -
187C PHE* 4.5 5.4 - - + -
197C ILE* 2.9 33.2 + - - +
200C ASP* 3.7 12.7 + - - +
201C ALA* 3.5 28.4 - - + +
204C ALA* 4.4 17.8 - - + +
205C ALA* 3.9 6.0 - - - +
209C HIS* 5.4 2.5 - - - +
102D THR* 3.4 27.7 + - - +
167D ARG* 3.2 30.2 - - - +
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Residues in contact with GLU 176 (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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172C GLN* 3.0 46.2 + - + +
173C VAL* 3.5 20.2 - - - +
175C ARG* 1.3 75.4 - - + +
177C LEU* 1.3 67.1 + - - +
179C SER* 2.6 26.9 + - - -
180C GLY 3.5 1.0 + - - -
209C HIS* 3.7 30.3 + - + +
210C HIS 3.3 23.0 + - - +
211C PHE* 3.8 21.1 - - + +
98D GLU* 4.7 1.0 - - - +
107D LYS* 4.0 13.2 + - - +
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Residues in contact with LEU 177 (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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146C PHE* 4.1 23.3 - - + +
148C ASP 3.4 24.0 - - - +
149C MET* 3.9 18.4 - - + +
152C PRO* 4.3 17.7 - - + -
164C ILE* 4.7 6.7 - - + -
173C VAL 2.8 13.5 + - - +
174C HIS* 3.3 13.9 - - + +
176C GLU* 1.3 75.3 - - - +
178C ALA* 1.3 58.9 + - - +
180C GLY* 2.8 21.9 + - - -
181C LEU* 3.3 23.3 + - + +
211C PHE* 3.7 30.4 - - + -
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Residues in contact with ALA 178 (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 ILE* 4.5 4.3 - - + -
174C HIS 3.1 8.5 + - - +
175C ARG 3.2 5.8 + - - +
177C LEU* 1.3 79.3 - - - +
179C SER* 1.3 58.9 + - - +
180C GLY 3.0 1.1 + - - -
181C LEU* 3.3 16.7 + - + +
185C VAL* 4.2 14.1 - - + -
187C PHE* 3.5 33.2 - - + -
205C ALA* 4.2 3.4 - - + -
228C ASN* 3.0 29.7 + - - +
231C CYS* 5.1 0.2 - - - -
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Residues in contact with SER 179 (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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175C ARG 3.1 10.7 + - - -
176C GLU 2.6 20.7 + - - -
178C ALA* 1.3 75.3 - - - +
180C GLY* 1.3 56.7 + - - +
205C ALA* 3.1 29.6 - - - +
207C HIS 3.3 15.0 + - - -
209C HIS* 3.8 9.1 - - - +
225C THR* 2.7 21.5 + - - +
226C GLY 4.1 0.2 + - - -
227C GLY 2.9 35.0 + - - +
228C ASN* 4.0 2.6 - - - +
11D LYS* 4.2 1.0 - - - +
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Residues in contact with GLY 180 (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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176C GLU 3.5 0.2 + - - -
177C LEU* 2.8 9.9 + - - -
179C SER* 1.3 82.9 + - - +
181C LEU* 1.3 61.8 + - - +
182C SER* 3.6 3.6 + - - -
211C PHE* 5.2 1.3 - - - -
225C THR* 3.4 22.2 - - - -
9D ASP* 5.5 0.2 - - - -
11D LYS* 3.9 9.5 - - - +
12D ILE* 3.4 26.3 - - - +
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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