Contacts of the strand formed by residues 210 - 214 (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 CYS 210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193A GLN* 2.9 11.1 + - - +
194A MET* 2.8 53.5 + - - -
206A CYS* 2.0 48.5 - - + -
209A GLY* 1.3 73.1 - - - +
211A LEU* 1.3 70.7 + - - +
299A TRP* 3.7 13.5 - - + +
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Residues in contact with LEU 211 (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 ILE* 4.4 17.3 - - + -
191A GLN* 3.7 25.8 - - + +
192A ILE 3.6 4.7 - - - +
193A GLN* 4.1 14.6 - - - +
194A MET* 4.6 2.2 - - - -
210A CYS* 1.3 88.9 - - - +
212A ALA* 1.3 59.4 + - - +
294A PRO 5.9 0.7 - - - +
295A THR 4.1 5.8 - - - +
296A GLY 5.8 0.7 - - - -
297A PRO 4.1 17.7 + - - +
298A THR* 3.1 16.6 - - + +
299A TRP* 2.8 32.2 + - - +
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Residues in contact with ALA 212 (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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191A GLN* 3.3 4.6 - - - -
192A ILE* 2.8 53.4 + - + +
194A MET* 4.1 24.9 - - + +
211A LEU* 1.3 72.7 - - - +
213A LEU* 1.3 59.7 + - - +
214A VAL 3.7 1.0 + - - -
262A LEU* 4.3 2.0 - - + -
299A TRP* 3.6 4.7 - - + -
301A LEU* 4.1 28.0 - - + -
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Residues in contact with LEU 213 (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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33A THR 5.2 0.7 - - - +
34A GLY* 4.6 9.4 - - - -
189A VAL* 3.7 27.6 - - + -
190A TRP* 3.6 19.1 - - + +
191A GLN* 4.0 6.1 - - + +
212A ALA* 1.3 70.9 - - - +
214A VAL* 1.3 57.0 + - - +
215A ASP* 3.4 22.4 + - + +
291A ILE* 5.3 1.6 - - + -
295A THR* 4.4 8.1 - - + -
298A THR* 3.6 12.8 - - + +
299A TRP 2.9 14.4 + - - +
300A ALA* 3.4 7.1 - - + -
301A LEU* 2.7 31.0 + - - +
391A 03D 3.8 41.1 - - + -
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Residues in contact with VAL 214 (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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33A THR* 2.7 25.6 + - - -
190A TRP* 3.0 14.2 + - - +
192A ILE* 4.2 15.3 - - + -
212A ALA 4.2 4.3 - - - +
213A LEU* 1.3 72.1 - - - +
215A ASP* 1.3 53.7 + - - +
216A THR 4.1 0.2 - - - -
301A LEU* 3.8 17.7 - - + +
305A PHE* 5.5 0.2 - - + -
306A ILE* 4.7 9.2 - - + -
311A THR* 4.1 2.2 - - + -
313A PHE* 3.9 22.8 - - + -
320A ILE* 3.3 30.1 - - + -
322A PHE* 4.0 36.3 - - + -
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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