Contacts of the helix formed by residues 184 - 196 (chain C) in PDB entry 4NEF
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 184 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20C THR* 5.1 0.6 - - - +
23C PHE* 3.4 24.1 - - + -
52C ILE* 5.1 2.4 - - - +
67C ILE 2.7 25.4 + - - -
68C ASN* 3.4 18.1 - - - +
69C PRO* 3.3 10.9 - - - +
182C SER* 2.8 20.2 + - - +
183C MET* 1.3 79.0 - - + +
185C PRO* 1.4 68.3 - - - +
186C ALA* 3.1 18.0 + - - +
187C ARG* 3.1 25.0 + - + +
188C SER 3.4 5.2 + - - -
204C PHE 4.6 0.2 - - - -
208C PRO* 4.1 0.2 - - - +
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Residues in contact with PRO 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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68C ASN* 3.5 14.1 - - - +
69C PRO* 3.9 8.7 - - + -
70C ALA* 3.9 19.7 - - + +
184C ASN* 1.4 82.9 - - - +
186C ALA* 1.4 55.5 + - - +
188C SER* 3.4 4.0 + - - -
189C LEU* 3.1 28.6 + - - +
204C PHE 3.6 19.0 - - - +
205C TRP* 3.7 48.4 + - + -
208C PRO* 3.9 11.2 - - + -
209C LEU* 4.5 7.4 - - + -
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Residues in contact with ALA 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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20C THR* 4.1 8.5 - - + -
69C PRO* 3.7 20.5 - - + +
93C GLN 3.9 14.1 - - - +
94C LEU* 4.1 12.8 - - + -
97C ALA* 3.3 28.2 - - + +
184C ASN* 3.1 11.5 + - - +
185C PRO* 1.4 73.9 - - - +
187C ARG* 1.4 58.7 + - - +
188C SER 3.2 0.4 - - - -
189C LEU* 4.1 1.0 - - - +
190C ALA* 3.1 25.6 + - - +
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Residues in contact with ARG 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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23C PHE* 4.1 13.9 - - + -
24C VAL* 4.0 15.6 - - + +
28C LEU* 3.5 20.5 - - + +
31C ALA* 5.4 1.2 - - - +
48C PHE* 3.7 35.9 - - + -
117C ALA* 2.8 34.9 + - - +
118C VAL 4.8 0.6 + - - -
119C ASN* 3.1 38.7 + - - +
172C HIS* 5.6 0.4 - - - -
180C GLY 4.2 7.3 + - - -
181C CYS 3.5 15.8 + - - -
182C SER* 3.9 10.5 - - - +
184C ASN* 3.1 24.7 + - + +
186C ALA* 1.4 77.0 - - - +
188C SER* 1.3 53.2 + - - +
190C ALA* 4.4 0.6 - - - +
191C PRO* 3.1 20.2 - - - +
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Residues in contact with SER 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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118C VAL* 5.3 0.5 - - - +
119C ASN* 2.7 21.9 + - - -
182C SER* 2.6 28.6 + - - -
184C ASN 3.4 1.6 + - - -
185C PRO* 3.6 10.3 - - - -
186C ALA 3.2 0.6 - - - -
187C ARG* 1.3 79.1 - - - +
189C LEU* 1.3 62.3 + - - +
191C PRO* 3.4 9.9 - - - +
192C ALA* 3.4 16.6 + - - +
201C HIS* 3.6 11.4 - - - -
204C PHE* 3.2 24.3 - - - +
205C TRP* 4.9 0.2 - - - -
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Residues in contact with LEU 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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94C LEU* 3.8 32.3 - - + -
98C VAL* 4.8 8.3 - - + -
185C PRO 3.1 16.5 + - - +
186C ALA* 3.5 4.2 + - - +
188C SER* 1.3 75.7 - - - +
190C ALA* 1.4 54.5 + - - +
192C ALA* 3.2 1.4 + - - +
193C VAL* 2.8 58.5 + - + +
198C PHE* 4.1 11.0 - - + -
201C HIS* 3.5 24.6 - - + +
205C TRP* 4.1 13.7 - - + -
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Residues in contact with ALA 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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24C VAL* 3.8 8.5 - - + -
97C ALA* 3.4 33.7 - - + +
98C VAL* 3.8 13.4 - - - +
101C ALA* 3.7 8.7 - - + -
186C ALA 3.1 17.8 + - - +
187C ARG 4.4 0.4 - - - +
189C LEU* 1.4 75.4 - - - +
191C PRO* 1.4 68.8 - - + +
193C VAL* 3.6 1.7 + - - +
194C VAL* 3.3 27.7 + - - +
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Residues in contact with PRO 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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28C LEU* 3.8 16.4 - - + -
101C ALA* 4.1 0.6 - - + -
116C LEU* 3.3 36.8 - - + +
118C VAL* 3.6 27.8 - - + -
187C ARG* 3.1 31.9 - - - +
188C SER 3.4 9.2 - - - +
190C ALA* 1.4 86.1 - - + +
192C ALA* 1.4 50.9 + - - +
194C VAL* 4.5 0.4 - - + -
195C THR* 2.7 41.6 + - - +
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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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118C VAL* 3.8 4.4 - - + +
188C SER 3.4 17.7 - - - +
189C LEU 3.2 5.7 + - - +
191C PRO* 1.4 78.2 - - - +
193C VAL* 1.4 56.8 + - - +
195C THR* 4.0 2.2 - - - -
196C GLY* 2.8 26.2 + - - -
197C LYS 3.1 23.1 + - - +
198C PHE* 3.2 32.0 - - + -
201C HIS* 3.9 9.4 - - + +
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Residues in contact with VAL 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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98C VAL* 4.2 20.2 - - + -
189C LEU* 2.8 44.2 + - + +
190C ALA 4.0 3.1 - - - +
192C ALA* 1.4 71.7 - - - +
194C VAL* 1.4 67.1 - - + +
195C THR 4.3 0.2 - - - -
196C GLY* 3.9 5.0 + - - -
198C PHE* 4.0 16.6 - - + -
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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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98C VAL* 4.0 8.1 - - + +
101C ALA* 3.8 9.2 - - + +
102C ALA* 3.7 30.1 - - + +
105C HIS* 4.1 21.3 - - + +
116C LEU* 3.9 22.2 - - + -
190C ALA 3.3 17.1 + - - +
191C PRO 4.1 1.8 - - - +
193C VAL* 1.4 82.4 - - + +
195C THR* 1.4 62.7 + - + +
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Residues in contact with THR 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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114C GLY 4.4 5.8 - - - +
115C ASP* 3.3 26.5 - - - +
116C LEU* 3.6 20.6 - - + -
118C VAL* 3.6 10.6 - - - +
191C PRO 2.7 29.5 + - - +
193C VAL 4.3 0.2 - - - -
194C VAL* 1.4 75.7 - - + +
196C GLY* 1.3 61.8 + - - -
197C LYS* 3.3 22.5 + - - +
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Residues in contact with GLY 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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192C ALA 2.8 18.3 + - - -
193C VAL 4.4 4.0 - - - -
194C VAL 3.7 0.8 - - - -
195C THR* 1.3 73.4 - - - +
197C LYS* 1.3 63.0 + - - +
198C PHE* 3.6 14.3 + - - -
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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