Contacts of the helix formed by residues 178 - 194 (chain C) in PDB entry 5SWW
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 178 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ILE* 3.8 16.6 - - - +
30B LYS* 4.7 2.6 - - - +
32B TYR* 4.7 1.0 + - - -
24C ASN* 3.6 2.5 - - - +
176C TRP* 3.4 1.2 + - - -
177C ASP* 1.3 72.5 - - - +
179C LEU* 1.3 64.7 + - - +
181C GLU* 3.2 27.5 + - - -
182C HIS* 2.5 38.0 + - - +
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Residues in contact with LEU 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LYS* 4.6 0.6 - - - +
24C ASN* 3.0 10.6 + - - -
154C THR 4.4 0.2 - - - -
155C TYR* 3.7 30.1 - - + +
158C PHE* 3.6 28.9 - - + -
173C PHE* 3.6 27.4 - - + -
175C PRO* 3.8 13.2 - - + -
176C TRP* 3.4 51.7 + - + +
177C ASP 3.4 0.8 + - - -
178C GLY* 1.3 75.7 - - - +
180C ASP* 1.3 72.5 + - - +
181C GLU* 3.5 0.6 + - - -
183C SER* 2.9 28.3 + - - -
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Residues in contact with ASP 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LYS* 2.9 22.3 + - - +
155C TYR* 4.1 3.6 + - - +
175C PRO* 5.1 1.2 - - - +
179C LEU* 1.3 86.2 - - - +
181C GLU* 1.3 60.4 + - - +
183C SER* 3.7 6.2 - - - -
184C GLN* 2.9 43.5 + - + +
1F G 3.1 25.1 + - - +
2F G 2.8 44.0 + - - +
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Residues in contact with GLU 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B HIS* 3.9 16.6 - - - +
17B ILE* 3.5 35.7 - - + +
20B SER* 3.6 23.8 + - - +
21B ASN* 3.3 17.5 + - - +
30B LYS* 3.1 34.7 + - - +
32B TYR* 3.8 8.1 + - - -
178C GLY* 3.2 23.3 + - - +
180C ASP* 1.3 70.2 - - - +
182C HIS* 1.3 63.6 + - - +
184C GLN* 3.1 5.6 + - - +
185C ALA* 2.9 22.5 + - - +
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Residues in contact with HIS 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ASP* 2.7 38.7 + - + -
16B HIS* 4.1 19.2 + + + -
17B ILE* 4.4 6.5 - - + -
24C ASN* 3.4 34.7 + - + +
25C GLY* 3.6 22.1 + - - -
177C ASP 5.1 1.8 - - - -
178C GLY* 2.5 37.1 + - - +
181C GLU* 1.3 78.8 - - - +
183C SER* 1.3 58.7 + - - +
185C ALA* 3.8 6.0 - - - +
186C LEU* 2.9 40.3 + - + +
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Residues in contact with SER 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C ASN* 3.6 5.8 - - - +
152C ILE* 3.9 5.1 - - - +
153C MET 2.9 26.7 + - - -
154C THR* 3.3 25.8 - - - +
179C LEU* 2.9 23.4 + - - -
180C ASP* 3.7 8.7 - - - -
181C GLU 3.2 0.2 - - - -
182C HIS* 1.3 77.2 - - - +
184C GLN* 1.3 55.0 + - - +
186C LEU* 5.2 0.4 - - - -
187C SER* 2.6 38.7 + - - -
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Residues in contact with GLN 184 (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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20B SER* 3.1 25.0 + - - -
28B ARG* 3.1 33.7 + - - +
180C ASP* 2.9 28.8 + - + +
181C GLU 3.1 2.7 + - - +
183C SER* 1.3 73.9 - - - +
185C ALA* 1.3 59.9 + - - +
187C SER* 3.3 6.1 + - - -
188C GLY* 2.9 25.5 + - - -
-2F A 3.0 38.4 + - - +
1F G 4.8 11.9 + - - +
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Residues in contact with ALA 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B HIS* 3.5 34.8 - - + +
181C GLU 2.9 14.9 + - - +
182C HIS* 3.8 4.7 - - - +
183C SER 3.4 0.2 - - - -
184C GLN* 1.3 76.2 - - - +
186C LEU* 1.3 61.5 + - + +
188C GLY* 3.1 3.6 + - - -
189C ARG* 2.9 34.9 + - + +
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Residues in contact with LEU 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B HIS* 6.4 0.2 - - - +
24C ASN* 4.6 11.4 - - + +
127C ALA 3.3 26.7 - - - +
128C ARG* 3.7 15.3 - - + -
129C ILE* 3.7 27.4 - - + +
152C ILE* 3.5 23.4 - - + +
182C HIS* 2.9 25.8 + - + +
183C SER* 5.3 0.2 - - - -
185C ALA* 1.3 78.6 - - + +
187C SER* 1.3 57.7 + - - +
189C ARG* 3.7 23.2 - - - +
190C LEU* 2.9 31.9 + - - +
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Residues in contact with SER 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C ILE* 3.6 22.3 + - - +
154C THR* 4.4 8.7 - - - +
183C SER* 2.6 29.8 + - - -
184C GLN* 3.6 7.4 - - - -
185C ALA 3.3 0.2 - - - -
186C LEU* 1.3 77.8 - - - +
188C GLY* 1.3 56.7 + - - +
190C LEU* 3.9 1.7 - - - +
191C ARG* 2.9 29.8 + - - +
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Residues in contact with GLY 188 (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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184C GLN 2.9 14.6 + - - -
185C ALA* 3.1 3.6 + - - -
187C SER* 1.3 75.2 - - - +
189C ARG* 1.3 59.1 + - - +
191C ARG* 3.2 10.5 + - - +
192C ALA* 2.9 28.1 + - - +
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Residues in contact with ARG 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B HIS* 6.1 2.9 - - - -
129C ILE* 4.0 15.3 + - + +
131C ASP* 3.5 29.7 + - - +
136C TYR* 3.1 41.2 + - - -
185C ALA* 2.9 20.7 + - - +
186C LEU* 3.3 30.1 + - - +
188C GLY* 1.3 76.3 - - - +
190C LEU* 1.3 57.6 + - - +
192C ALA* 3.0 9.2 + - - +
193C ILE* 2.9 36.6 + - + +
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Residues in contact with LEU 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C ILE* 4.4 3.4 - - + +
140C LEU* 3.7 31.9 - - + -
150C VAL* 3.5 30.7 - - + +
151C SER* 3.6 17.9 - - - -
152C ILE* 3.7 21.8 - - + +
186C LEU 2.9 16.9 + - - +
187C SER* 4.0 2.9 - - - +
189C ARG* 1.3 75.9 - - - +
191C ARG* 1.3 63.3 + - - +
193C ILE* 4.2 6.3 - - + -
194C LEU* 3.0 49.9 + - + +
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Residues in contact with ARG 191 (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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187C SER 2.9 21.8 + - - +
188C GLY* 3.2 10.5 + - - +
190C LEU* 1.3 76.3 - - - +
192C ALA* 1.3 60.2 + - - +
194C LEU* 4.0 7.0 + - - +
195C GLN* 3.4 23.8 + - - +
101F GOL 4.3 30.1 + - - -
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Residues in contact with ALA 192 (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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188C GLY 2.9 13.4 + - - +
189C ARG* 3.5 9.4 - - - +
191C ARG* 1.3 74.8 - - - +
193C ILE* 1.3 65.3 + - + +
195C GLN* 3.6 29.0 - - - +
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Residues in contact with ILE 193 (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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129C ILE* 5.1 2.2 - - + -
136C TYR* 3.9 12.6 - - + +
137C LYS* 3.6 57.0 - - + +
140C LEU* 3.8 25.1 - - + -
141C GLN* 3.3 29.9 + - + +
144C ARG* 4.6 0.9 + - - -
189C ARG* 2.9 29.5 + - + +
190C LEU* 3.1 7.2 + - + +
192C ALA* 1.3 80.4 - - + +
194C LEU* 1.3 63.9 + - + +
195C GLN* 3.1 7.0 + - - +
196C ASN* 4.9 1.9 + - - +
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Residues in contact with LEU 194 (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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140C LEU 3.9 27.6 - - - +
141C GLN* 4.0 5.6 - - - +
144C ARG* 3.3 44.6 + - + +
150C VAL* 4.0 24.5 - - + +
190C LEU* 3.0 42.0 + - + +
191C ARG* 4.2 4.5 - - - +
192C ALA 3.5 0.4 - - - -
193C ILE* 1.3 82.6 - - + +
195C GLN* 1.3 60.1 + - - +
196C ASN 3.8 0.5 + - - -
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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
------------------------------------------------------------
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