Contacts of the helix formed by residues 184 - 191 (chain A) in PDB entry 4NAM
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 184 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A TYR* 3.7 26.9 - - + -
32A PRO* 4.3 17.9 - - + -
35A VAL* 4.0 12.6 - - + -
175A VAL* 4.1 16.6 - - + -
176A PRO* 3.3 13.2 - - + +
177A ASP* 4.7 2.0 - - + -
182A GLY 3.5 8.7 - - - +
183A ILE* 1.3 92.3 - - + +
185A ASP* 1.3 67.5 + - - +
186A SER* 4.4 6.3 - - - +
187A LEU* 3.1 25.7 + - + +
188A GLU* 3.2 9.5 + - - +
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Residues in contact with ASP 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A PRO* 2.9 36.8 + - + +
177A ASP* 3.3 2.8 - - - +
178A ARG* 2.9 55.1 + - - +
183A ILE 3.4 1.4 + - - +
184A PRO* 1.3 70.3 - - - +
186A SER* 1.3 64.1 + - - +
188A GLU* 3.2 4.4 + - - +
189A VAL* 3.1 28.8 + - + +
223A PRO* 3.8 21.1 - - + +
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Residues in contact with SER 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A GLN 4.6 5.6 + - - -
32A PRO* 4.0 25.3 - - - +
184A PRO* 4.4 3.6 - - - +
185A ASP* 1.3 79.6 - - - +
187A LEU* 1.3 60.8 + - - +
189A VAL* 3.5 4.2 + - - -
190A GLU* 2.9 52.1 + - - +
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Residues in contact with LEU 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A PRO* 3.9 34.3 - - + +
35A VAL* 4.1 7.9 - - + -
183A ILE* 4.2 8.7 - - + -
184A PRO* 3.1 21.9 + - + +
186A SER* 1.3 81.1 + - - +
188A GLU* 1.3 65.2 + - - +
190A GLU* 4.5 3.1 - - + +
191A GLY 2.9 25.2 + - - +
192A TYR* 3.2 18.5 - - + -
203A LEU* 3.7 24.2 - - + +
204A SER 4.3 0.9 - - - -
205A PRO* 3.7 44.4 - - + -
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Residues in contact with GLU 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A ASP* 3.4 2.6 - - - +
181A ASP* 3.3 4.2 - - - +
183A ILE* 3.3 25.4 - - + -
184A PRO 3.2 5.4 + - - +
185A ASP 3.6 6.7 - - - +
187A LEU* 1.3 77.4 - - - +
189A VAL* 1.3 62.2 + - - +
192A TYR* 3.8 8.3 - - - -
220A LYS* 3.5 8.0 - - - +
221A SER* 2.7 53.5 + - - +
222A SER 2.9 7.9 - - - +
223A PRO* 3.4 11.0 - - + +
235A ASP* 3.1 3.8 - - - +
801A CA 2.3 27.9 - - - -
802A CA 2.3 31.9 - - - -
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Residues in contact with VAL 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A ASP* 3.1 17.9 + - + +
186A SER* 4.0 4.5 - - - +
188A GLU* 1.3 80.6 - - - +
190A GLU* 1.3 69.1 + - + +
220A LYS* 3.8 16.8 - - - +
221A SER 4.5 1.6 - - - +
223A PRO* 3.7 28.5 - - + -
517A THR 5.5 1.6 - - - +
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Residues in contact with GLU 190 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186A SER* 2.9 35.5 + - - +
187A LEU* 5.0 2.7 - - + +
189A VAL* 1.3 85.6 - - + +
191A GLY* 1.3 61.6 + - - +
206A TYR* 5.5 2.3 - - - +
218A LYS* 4.6 4.9 + - - -
220A LYS* 3.7 12.6 - - - +
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Residues in contact with GLY 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A LEU* 2.9 14.4 + - - +
189A VAL 3.5 1.8 - - - -
190A GLU* 1.3 83.1 - - - +
192A TYR* 1.3 62.3 + - - +
205A PRO* 3.5 8.5 - - - +
206A TYR* 3.0 25.9 + - - +
218A LYS* 4.8 4.0 - - - -
219A TYR 3.2 14.1 - - - -
220A LYS* 3.9 8.3 - - - +
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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