Contacts of the helix formed by residues 194 - 205 (chain D) in PDB entry 4NH1
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 PRO 194 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A GLN* 4.1 4.5 - - - +
192D ILE 3.5 4.2 - - - +
193D HIS* 1.3 103.0 - - + +
195D MET* 1.3 61.8 + - - +
196D ALA 3.1 0.7 - - - -
197D TYR* 3.3 26.3 + - + +
198D GLN* 3.4 10.4 + - - +
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Residues in contact with MET 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A VAL* 3.9 19.7 - - + -
57A ILE* 4.6 7.2 - - + -
193D HIS* 3.0 23.6 + - + +
194D PRO* 1.3 76.5 - - - +
196D ALA* 1.3 65.4 + - - +
198D GLN* 3.1 20.9 + - + +
199D LEU* 2.9 49.2 + - + +
202D GLN* 5.4 2.7 - - - +
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Residues in contact with ALA 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A VAL* 3.2 35.4 - - - +
169C MET* 4.2 8.5 - - + -
192D ILE* 3.7 19.1 - - + -
193D HIS 2.9 14.8 + - - +
195D MET* 1.3 79.2 - - - +
197D TYR* 1.3 60.7 + - + +
199D LEU* 3.4 3.3 + - - +
200D GLN* 3.1 36.0 + - - +
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Residues in contact with TYR 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C TYR* 4.1 7.3 + - - -
141C MET* 3.6 43.5 - - + -
165C HIS* 4.7 3.5 + - - -
175C ARG* 3.7 28.5 - - - +
185D PRO* 3.5 27.8 - - + +
192D ILE* 3.6 40.9 - - + +
193D HIS 4.0 2.5 - - - -
194D PRO* 3.3 21.1 + - + +
195D MET 3.2 0.6 - - - -
196D ALA* 1.3 73.9 - - + +
198D GLN* 1.3 64.4 + - - +
200D GLN* 3.6 9.4 + - - +
201D LEU* 3.2 31.7 + - + +
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Residues in contact with GLN 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194D PRO 3.4 10.2 + - - +
195D MET* 3.1 25.9 + - + +
197D TYR* 1.3 77.8 - - - +
199D LEU* 1.3 63.7 + - - +
201D LEU* 3.4 17.1 + - - +
202D GLN* 3.1 58.6 + - - +
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Residues in contact with LEU 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A VAL* 3.7 31.9 - - + +
43A ARG* 4.2 26.0 - - + -
55A GLU* 5.7 1.6 - - - +
172C PRO* 5.3 0.2 - - - -
195D MET* 2.9 40.8 + - + +
196D ALA 3.8 4.5 - - - +
198D GLN* 1.3 76.5 - - - +
200D GLN* 1.3 59.5 + - + +
202D GLN* 3.3 20.7 + - - +
203D ALA* 3.0 27.9 + - - +
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Residues in contact with GLN 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A VAL 5.3 0.4 + - - -
165C HIS 4.9 1.6 + - - -
168C PHE* 3.4 37.0 + - - +
169C MET* 4.2 19.6 - - - +
172C PRO* 2.9 28.3 - - + +
175C ARG* 2.7 54.2 + - + +
196D ALA* 3.1 26.6 + - - +
197D TYR* 3.9 8.8 - - - +
198D GLN 3.3 0.2 - - - -
199D LEU* 1.3 76.5 - - + +
201D LEU* 1.3 58.3 + - - +
203D ALA* 3.4 0.5 + - - +
204D ALA* 2.9 24.3 + - - +
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Residues in contact with LEU 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C MET* 5.9 6.1 - - + -
175C ARG* 3.7 16.8 - - + +
176C PRO 3.4 28.7 - - - +
177C LYS* 4.3 13.3 - - + -
178C ARG* 4.5 26.2 - - + +
197D TYR* 3.2 22.6 + - + +
198D GLN* 3.7 19.1 - - - +
200D GLN* 1.3 75.0 - - - +
202D GLN* 1.3 60.1 + - + +
204D ALA* 3.2 6.2 + - + +
205D SER* 3.1 31.4 + - - -
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Residues in contact with GLN 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195D MET* 5.4 2.8 - - - +
198D GLN* 3.1 46.7 + - - +
199D LEU* 3.7 22.2 - - - +
201D LEU* 1.3 77.9 - - + +
203D ALA* 1.3 59.6 + - - +
205D SER* 3.4 12.4 + - - -
206D ASN* 3.0 23.5 + - - +
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Residues in contact with ALA 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C PRO* 3.8 23.6 - - + -
173C GLU* 4.2 11.6 - - + +
199D LEU 3.0 16.6 + - - +
200D GLN 3.6 5.4 - - - +
201D LEU 3.2 0.2 - - - -
202D GLN* 1.3 76.5 - - - +
204D ALA* 1.3 62.1 + - - +
206D ASN* 3.4 25.0 + - - +
207D PHE 4.3 3.6 + - - +
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Residues in contact with ALA 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C PRO 3.9 4.7 - - - +
173C GLU* 4.0 18.2 - - - +
175C ARG 3.3 24.5 - - - +
177C LYS* 2.9 22.0 + - + +
200D GLN 2.9 17.1 + - - +
201D LEU* 3.2 9.8 + - + +
203D ALA* 1.3 74.6 - - - +
205D SER* 1.3 55.1 - - - +
206D ASN 3.1 9.4 + - - -
207D PHE* 3.6 17.3 + - - +
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Residues in contact with SER 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177C LYS* 3.3 22.6 - - - +
201D LEU 3.1 15.1 + - - -
202D GLN* 3.8 8.2 - - - -
203D ALA 3.2 1.2 - - - -
204D ALA* 1.3 76.4 - - - +
206D ASN* 1.3 64.2 + - - +
207D PHE* 3.7 3.8 - - - -
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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