Contacts of the helix formed by residues 180 - 196 (chain C) in PDB entry 4CYM
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 ASN 180 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171C PHE* 4.1 16.4 - - + +
172C GLU* 2.9 32.4 + - - +
173C THR* 4.2 4.5 - - + +
178C ASN 3.9 2.2 + - - -
179C ILE* 1.3 81.7 - - - +
181C ILE* 1.3 59.1 + - - +
183C GLU* 3.3 33.8 + - - +
184C ALA* 3.0 29.6 + - - +
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Residues in contact with ILE 181 (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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41C ILE* 4.3 28.5 - - + -
44C ARG* 3.9 18.6 - - + -
45C TYR* 3.6 36.8 - - + -
141C LEU* 6.3 0.7 - - + -
173C THR* 4.3 12.1 - - + -
174C SER 3.7 20.6 - - - +
175C ALA* 3.8 16.8 - - - +
178C ASN* 4.2 8.8 + - - +
179C ILE 3.2 9.8 - - - +
180C ASN* 1.3 75.5 - - - +
182C GLU* 1.3 68.8 + - + +
183C GLU 3.0 1.4 + - - -
184C ALA* 3.1 4.9 + - - +
185C ALA* 2.9 24.6 + - + +
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Residues in contact with GLU 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C TYR* 3.6 31.3 + - + -
48C GLN* 4.2 13.8 + - - +
65C LYS* 4.6 6.9 + - - -
67C LEU* 5.7 2.6 - - - +
178C ASN* 4.8 15.4 + - - +
181C ILE* 1.3 78.4 - - + +
183C GLU* 1.3 68.0 + - - +
185C ALA* 3.5 2.4 - - - +
186C ARG* 3.0 44.0 + - - +
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Residues in contact with GLU 183 (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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171C PHE* 3.9 15.3 - - + -
180C ASN* 3.3 40.6 + - - +
181C ILE 3.0 1.1 + - - -
182C GLU* 1.3 85.4 - - - +
184C ALA* 1.3 61.9 + - - +
186C ARG* 3.3 7.5 + - - +
187C PHE* 2.8 28.4 + - - +
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Residues in contact with ALA 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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103C PHE* 3.9 9.5 - - + -
139C VAL* 4.9 0.2 - - - +
141C LEU* 3.8 21.1 - - + -
171C PHE* 3.6 35.0 - - + -
173C THR* 5.0 0.4 - - + -
180C ASN 3.0 19.7 + - - +
181C ILE* 3.7 3.8 - - - +
183C GLU* 1.3 74.4 - - - +
185C ALA* 1.3 65.3 + - - +
187C PHE* 3.3 3.1 + - - +
188C LEU* 3.0 24.4 + - - +
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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
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45C TYR* 3.3 44.4 - - + +
77C LEU* 5.4 4.3 - - + -
103C PHE* 3.9 16.8 - - + -
181C ILE* 2.9 17.2 + - + +
182C GLU 3.5 4.0 - - - +
184C ALA* 1.3 74.9 - - - +
186C ARG* 1.3 62.6 + - - +
188C LEU* 3.1 4.2 + - - +
189C VAL* 2.9 29.1 + - - +
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Residues in contact with ARG 186 (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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67C LEU* 6.0 6.1 - - - +
68C ASN 5.1 7.5 + - - -
69C TRP* 3.6 45.4 + - + -
182C GLU* 3.0 31.9 + - - +
183C GLU* 3.6 6.3 - - - +
185C ALA* 1.3 78.6 - - - +
187C PHE* 1.3 63.8 + - - +
188C LEU 3.2 0.3 + - - -
189C VAL* 3.2 3.6 + - - +
190C GLU* 3.0 38.1 + - - +
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Residues in contact with PHE 187 (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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160A GLN* 3.9 24.6 - - - +
163A LYS* 4.2 30.1 - - + -
164A GLU* 4.7 3.4 - - - -
139C VAL* 3.8 16.4 - - + -
168C ALA* 3.2 43.7 - - + -
169C GLY* 4.0 9.6 - - - -
171C PHE* 3.5 25.1 - + + -
183C GLU 2.8 17.7 + - - +
184C ALA 3.5 7.6 - - - +
185C ALA 3.3 0.2 - - - -
186C ARG* 1.3 71.5 - - - +
188C LEU* 1.3 66.2 + - - +
190C GLU* 3.5 15.8 - - - +
191C LYS* 3.3 18.8 + - + +
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Residues in contact with LEU 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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28C VAL* 3.8 22.0 - - + -
101C GLY* 4.5 0.4 - - - -
102C ALA 4.0 13.7 - - - +
103C PHE* 3.6 32.5 - - + -
137C PRO* 3.9 29.6 - - + +
139C VAL* 3.9 19.7 - - + -
184C ALA 3.0 17.4 + - - +
185C ALA 3.6 4.0 - - - +
187C PHE* 1.3 81.6 - - - +
189C VAL* 1.3 65.4 + - + +
191C LYS* 2.9 18.5 + - + +
192C ILE* 2.9 27.9 + - + +
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Residues in contact with VAL 189 (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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26C PHE* 4.8 2.7 - - + -
67C LEU* 4.3 11.7 - - + -
69C TRP* 3.8 21.8 - - + -
75C VAL* 4.6 13.5 - - + -
77C LEU* 4.1 34.3 - - + -
185C ALA 2.9 21.9 + - - +
186C ARG* 3.7 4.0 - - - +
188C LEU* 1.3 77.5 - - + +
190C GLU* 1.3 52.8 + - - +
192C ILE* 3.1 13.4 + - + +
193C LEU* 2.8 54.0 + - + +
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Residues in contact with GLU 190 (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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160A GLN* 3.6 15.2 - - - +
163A LYS* 3.1 44.6 + - - +
69C TRP* 3.8 21.7 - - + -
186C ARG* 3.0 32.7 + - - +
187C PHE* 3.5 17.0 - - - +
189C VAL* 1.3 75.8 - - - +
191C LYS* 1.3 63.9 + - - +
193C LEU* 3.1 6.4 + - - +
194C VAL* 2.9 28.3 + - + +
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Residues in contact with LYS 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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160A GLN* 3.2 37.2 + - + +
164A GLU* 3.0 23.9 + - - +
137C PRO* 3.7 26.6 - - + +
168C ALA* 3.6 21.5 - - + -
187C PHE* 3.3 11.1 + - + +
188C LEU* 2.9 16.2 + - + +
190C GLU* 1.3 76.3 - - - +
192C ILE* 1.3 61.5 - - - +
194C VAL* 3.5 8.4 + - - +
195C ASN* 3.2 39.4 + - - +
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Residues in contact with ILE 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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26C PHE* 3.5 44.2 - - + -
28C VAL* 4.2 17.3 - - + -
100C VAL* 3.4 31.2 - - + +
101C GLY* 4.1 7.0 - - - -
137C PRO* 4.0 7.4 - - + -
188C LEU* 2.9 37.6 + - + +
189C VAL* 3.3 11.7 - - + +
191C LYS* 1.3 78.4 - - - +
193C LEU* 1.3 62.8 + - - +
195C ASN* 3.1 21.0 + - - +
196C HIS* 3.1 17.3 + - + -
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Residues in contact with LEU 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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24C HIS* 3.8 31.6 - - + +
26C PHE* 4.0 18.8 - - + -
69C TRP* 3.3 44.4 - - + +
73C THR* 5.2 3.1 - - + -
75C VAL* 4.8 3.8 - - + -
189C VAL* 2.8 28.6 + - + +
190C GLU* 3.5 7.6 - - - +
192C ILE* 1.3 73.8 - - - +
194C VAL* 1.3 62.8 + - + +
196C HIS* 3.1 15.9 + - + +
197C GLN* 3.2 15.6 + - - +
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Residues in contact with VAL 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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156A SER* 3.7 36.6 - - - +
157A GLN* 4.1 23.7 - - + +
160A GLN* 4.1 20.2 - - + -
190C GLU* 2.9 20.3 + - + +
191C LYS* 3.6 11.2 - - - +
193C LEU* 1.3 78.1 - - + +
195C ASN* 1.3 61.7 + - - +
197C GLN* 3.2 25.0 + - - +
198C SER* 3.2 10.0 + - - +
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Residues in contact with ASN 195 (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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100C VAL 4.8 0.4 + - - -
130C LEU* 4.0 23.2 - - + +
132C ASN* 6.1 0.4 - - - +
137C PRO* 3.7 33.9 - - - +
191C LYS* 3.2 31.1 + - - +
192C ILE* 3.1 10.1 + - - +
194C VAL* 1.3 80.1 - - - +
196C HIS* 1.3 65.3 + - + +
197C GLN 3.2 1.1 - - - -
198C SER* 3.2 29.7 + - - +
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Residues in contact with HIS 196 (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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24C HIS* 5.5 11.2 + - + +
26C PHE* 4.2 19.2 - + + -
100C VAL* 3.7 30.0 - - + +
130C LEU* 4.9 8.5 - - + +
131C PRO* 6.0 4.9 - - + +
192C ILE* 3.1 28.6 + - + +
193C LEU* 3.1 12.3 + - + +
195C ASN* 1.3 82.4 - - + +
197C GLN* 1.3 55.9 + - - +
198C SER 3.7 0.9 - - - -
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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