Contacts of the strand formed by residues 191 - 199 (chain A) in PDB entry 1HRN
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 GLN 191 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184A LEU* 3.7 5.3 - - - +
185A ILE* 3.2 35.2 + - + +
186A LYS* 5.6 2.0 - - - +
189A VAL* 2.9 33.0 + - + +
190A TRP* 1.3 73.4 - - - +
192A ILE* 1.3 72.9 + - - +
211A LEU* 3.7 18.8 - - + +
212A ALA 3.3 16.8 - - - +
213A LEU* 4.0 4.8 - - + +
294A PRO 5.6 0.6 + - - -
295A THR* 3.1 29.6 + - - +
298A THR* 2.8 28.2 + - + +
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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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182A ILE* 3.9 45.1 - - + +
183A ASN 3.8 15.9 - - - +
184A LEU* 4.0 4.3 - - + -
185A ILE* 4.1 7.6 - - - -
191A GLN* 1.3 81.3 - - - +
193A GLN* 1.3 61.5 + - - +
211A LEU* 3.6 4.0 - - - -
212A ALA* 2.8 48.2 + - + +
214A VAL* 4.2 15.0 - - + -
262A LEU* 3.8 27.8 - - + -
301A LEU* 5.5 0.4 - - + -
320A ILE* 4.0 20.0 - - + -
322A PHE* 4.3 2.5 - - + -
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Residues in contact with GLN 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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182A ILE* 4.2 8.1 - - + +
183A ASN 4.9 2.5 + - - +
185A ILE* 3.8 27.7 - - + +
192A ILE* 1.3 78.4 - - - +
194A MET* 1.3 60.8 + - - +
195A LYS* 2.5 43.4 + - + +
209A GLY* 3.6 9.1 - - - -
210A CYS* 2.9 37.9 + - - +
211A LEU* 4.1 5.5 - - - +
262A LEU* 3.9 7.4 - - - +
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Residues in contact with MET 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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192A ILE 3.7 0.4 + - - -
193A GLN* 1.3 75.7 + - - +
195A LYS* 1.3 66.2 + - - +
196A GLY 3.7 11.2 - - - +
197A VAL* 3.6 22.0 - - + -
206A CYS* 3.2 2.1 - - - -
209A GLY* 3.3 2.4 - - - -
210A CYS* 2.8 52.0 + - - +
211A LEU 4.3 0.2 - - - +
212A ALA* 4.1 14.6 - - + -
260A PHE* 3.9 24.9 - - + -
261A HIS 3.5 11.7 - - - +
262A LEU* 3.6 14.4 - - + -
299A TRP* 3.3 48.9 - - + -
301A LEU* 5.2 2.0 - - + -
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Residues in contact with LYS 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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182A ILE* 4.2 5.1 - - - +
193A GLN* 2.5 50.2 + - + +
194A MET* 1.3 73.5 - - - +
196A GLY* 1.3 54.9 + - - +
203A THR* 5.5 0.5 - - - +
206A CYS 3.1 10.7 - - - +
207A GLU* 4.8 1.2 - - - -
208A ASP 4.5 2.4 + - - -
209A GLY* 3.9 8.6 + - - -
261A HIS* 2.7 40.9 + - + +
262A LEU* 3.8 2.8 - - - +
263A GLY* 2.8 41.1 - - - +
264A GLY 4.4 6.3 - - - +
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Residues in contact with GLY 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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194A MET* 3.4 4.8 - - - +
195A LYS* 1.3 81.0 - - - +
197A VAL* 1.3 69.6 + - - +
198A SER 4.3 0.2 - - - -
203A THR* 4.5 8.5 - - - -
205A LEU 3.8 1.6 - - - -
206A CYS* 3.2 18.6 - - - -
261A HIS* 2.9 34.6 + - - +
266A GLU* 5.0 0.7 - - - -
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Residues in contact with VAL 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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194A MET* 3.6 32.5 - - + -
196A GLY* 1.3 81.1 - - - +
198A SER* 1.4 64.6 + - - +
203A THR* 3.6 4.6 - - - +
204A LEU* 3.2 5.5 + - - +
205A LEU* 2.9 56.9 + - + +
206A CYS* 4.0 6.3 - - + -
231A LEU* 5.0 0.9 - - + -
258A ILE* 4.2 7.9 - - + -
259A SER 3.3 13.9 - - - +
260A PHE* 4.0 19.3 - - + -
299A TRP* 4.3 18.4 - - + -
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Residues in contact with SER 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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196A GLY 4.3 0.2 - - - -
197A VAL* 1.4 73.2 - - - +
199A VAL* 1.3 61.7 + - - +
200A GLY 3.8 3.3 + - - -
201A SER* 3.0 32.2 + - - -
202A SER 3.5 3.6 - - - -
203A THR* 3.2 13.7 + - - +
258A ILE* 3.4 8.8 - - - +
259A SER* 3.0 46.4 + - - -
266A GLU* 4.5 7.4 + - - -
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Residues in contact with VAL 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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197A VAL* 5.5 0.2 - - + -
198A SER* 1.3 74.0 - - - +
200A GLY* 1.3 59.0 + - - +
201A SER 3.4 0.7 + - - -
202A SER* 3.3 26.0 + - - -
204A LEU* 4.1 27.8 - - + +
205A LEU* 4.3 3.8 - - + -
231A LEU* 3.2 34.3 - - + -
234A ALA* 4.1 15.0 - - + -
235A LEU* 3.8 28.9 - - + -
256A PRO* 3.8 13.4 - - + +
257A ASP 3.7 4.3 - - - +
258A ILE* 4.5 3.4 - - + +
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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