Contacts of the helix formed by residues 185 - 200 (chain A) in PDB entry 5FN4
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 ASP 185 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A LYS* 5.0 6.6 - - + +
125A LEU* 5.3 6.9 - - - +
127A LYS* 5.4 6.7 + - - +
183A LEU 3.5 9.3 + - - +
184A GLU* 1.3 84.1 - - - +
186A GLU* 1.3 69.5 + - - +
187A ASN* 3.3 32.8 + - - +
188A GLU* 4.0 17.2 + - - +
189A THR* 4.0 5.4 - - - +
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Residues in contact with GLU 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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99A GLU* 4.7 7.4 - - - +
124A SER* 4.4 10.6 + - - +
125A LEU 5.0 9.5 + - - +
126A THR* 5.6 4.0 - - - +
127A LYS* 4.5 31.5 + - - +
185A ASP* 1.3 74.9 + - - +
187A ASN* 1.3 59.2 - - - +
188A GLU 3.2 1.8 - - - -
189A THR* 2.5 37.7 + - - +
190A LYS* 2.9 15.7 + - + +
193A LYS* 5.9 0.9 + - - -
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Residues in contact with ASN 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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185A ASP* 3.3 23.4 + - - +
186A GLU* 1.3 76.3 - - - +
188A GLU* 1.3 58.5 + - + +
190A LYS* 3.2 14.0 + - - +
191A VAL* 2.9 34.6 + - + +
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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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44A LEU* 3.6 26.8 - - + +
45A ASN* 4.1 8.2 + - + +
46A LYS* 2.8 57.5 + - - +
47A THR* 4.3 0.7 + - - +
183A LEU* 3.6 18.7 - - + +
184A GLU 3.5 11.9 - - - +
185A ASP* 4.0 13.2 + - - +
187A ASN* 1.3 76.1 - - - +
189A THR* 1.3 57.7 + - - +
191A VAL* 3.2 9.5 + - - +
192A ILE* 2.9 35.2 + - - +
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Residues in contact with THR 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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97A LEU* 4.5 12.3 - - + +
99A GLU* 5.3 2.0 + - - -
124A SER* 3.0 39.8 + - - +
183A LEU* 4.1 16.8 - - + +
185A ASP 4.0 15.0 - - - +
186A GLU* 2.5 33.1 + - - +
188A GLU* 1.3 81.3 - - - +
190A LYS* 1.3 54.9 + - - +
192A ILE* 3.2 9.9 + - - +
193A LYS* 2.9 38.9 + - - +
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Residues in contact with LYS 190 (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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186A GLU* 2.9 11.1 + - + +
187A ASN* 3.2 19.0 + - - +
189A THR* 1.3 82.7 + - - +
191A VAL* 1.3 60.2 + - + +
193A LYS* 3.2 12.8 + - + +
194A GLN* 2.9 40.7 + - + +
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Residues in contact with VAL 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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42A ILE* 5.2 13.9 - - + -
44A LEU* 5.9 1.8 - - + -
187A ASN* 2.9 17.6 + - + +
188A GLU* 3.2 13.7 + - - +
190A LYS* 1.3 78.9 - - + +
192A ILE* 1.3 65.3 + - + +
194A GLN* 3.2 18.7 + - - +
195A CYS* 2.9 28.8 + - + +
660A ILE* 5.0 12.3 - - + -
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Residues in contact with ILE 192 (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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44A LEU* 3.7 23.6 - - + -
73A ILE* 3.6 14.7 - - + +
75A VAL* 5.2 2.7 - - + -
97A LEU* 3.3 26.2 - - + -
183A LEU* 3.7 30.5 - - + -
188A GLU 2.9 16.0 + - - +
189A THR 3.5 7.0 - - - +
191A VAL* 1.3 79.3 - - + +
193A LYS* 1.3 57.0 + - - +
195A CYS* 3.2 8.2 + - - +
196A TYR* 2.9 27.5 + - - +
215A MET* 4.0 5.2 - - + -
660A ILE* 3.4 34.3 - - + -
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Residues in contact with LYS 193 (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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75A VAL* 4.0 22.9 - - + -
77A GLU* 4.6 16.2 + - - +
97A LEU* 4.7 8.5 - - + -
99A GLU* 3.7 35.2 + - - +
186A GLU* 5.9 0.8 + - - -
189A THR* 2.9 22.8 + - - +
190A LYS* 3.4 12.6 - - + +
192A ILE* 1.3 75.3 - - - +
194A GLN* 1.3 58.9 + - - +
196A TYR* 3.2 7.6 + - - +
197A GLN* 2.6 44.4 + - - +
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Residues in contact with GLN 194 (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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190A LYS* 2.9 25.1 + - + +
191A VAL* 3.3 21.6 - - - +
193A LYS* 1.3 77.7 - - - +
195A CYS* 1.3 57.6 + - - +
197A GLN* 3.2 8.5 + - + +
198A ASP* 2.9 46.0 + - - +
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Residues in contact with CYS 195 (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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73A ILE* 4.3 0.4 - - + -
191A VAL* 2.9 14.3 + - + +
192A ILE* 3.3 11.2 - - - +
194A GLN* 1.3 78.8 + - - +
196A TYR* 1.3 62.7 + - - +
198A ASP* 3.2 11.2 + - - +
199A HIS* 3.1 32.1 + - - +
213A CYS* 2.1 49.0 - - - +
660A ILE* 5.1 4.5 - - + -
662A LEU* 4.7 0.2 - - - -
149C ILE* 3.4 28.3 - - + -
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Residues in contact with TYR 196 (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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73A ILE* 3.2 41.7 - - + +
74A HIS* 3.1 40.3 + - - -
75A VAL* 3.7 34.8 + - + +
192A ILE 2.9 12.6 + - - +
193A LYS* 3.2 11.6 + - - +
195A CYS* 1.3 76.1 - - - +
197A GLN* 1.3 78.4 + - - +
199A HIS 3.1 0.2 + - - -
200A ASN* 2.9 51.5 + - + -
201A LEU* 3.4 29.8 - - + +
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Residues in contact with GLN 197 (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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75A VAL* 5.4 3.9 - - - +
193A LYS* 2.6 36.8 + - - +
194A GLN* 3.3 12.3 - - + +
196A TYR* 1.3 98.4 - - - +
198A ASP* 1.3 64.5 + - - +
201A LEU* 3.0 30.7 - - + +
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Residues in contact with ASP 198 (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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194A GLN* 2.9 35.6 + - - +
195A CYS* 3.3 6.7 - - - +
197A GLN* 1.3 80.4 - - - +
199A HIS* 1.3 85.8 + - + +
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Residues in contact with HIS 199 (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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195A CYS* 3.1 16.2 + - - +
196A TYR 3.1 6.4 + - - -
197A GLN 4.6 1.1 - - - -
198A ASP* 1.3 102.2 + - + +
200A ASN* 1.3 72.3 + - - +
201A LEU* 3.1 14.1 + - - +
203A GLN* 5.9 1.0 + - - -
209A THR* 4.2 21.6 - - + +
211A PRO* 3.3 26.1 + - + +
212A LEU* 4.2 6.3 - - + -
213A CYS* 3.6 14.8 - - + +
662A LEU* 3.5 31.5 - - + +
148C GLY 5.8 0.4 + - - -
149C ILE* 5.8 1.2 + - - +
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Residues in contact with ASN 200 (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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72A VAL* 3.2 23.4 - - + +
73A ILE* 2.7 42.6 + - - +
74A HIS* 6.0 0.2 - - - +
84A TRP* 5.5 6.2 - - - -
196A TYR* 2.9 35.9 + - + -
199A HIS* 1.3 73.2 - - - +
201A LEU* 1.3 63.5 + - - +
208A PRO* 3.8 13.2 - - - +
212A LEU* 3.8 12.6 - - + +
213A CYS* 2.9 29.3 + - - +
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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