Contacts of the strand formed by residues 214 - 219 (chain A) in PDB entry 1OWH
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 214 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A TRP* 4.0 20.2 - - + +
15A PHE* 3.8 24.2 - - + -
37A GLY 4.2 0.9 - - - +
38A SER* 3.2 24.2 - - - +
148A GLU 3.7 1.0 - - - +
149A ILE* 3.5 24.5 - - - +
150A THR* 3.9 17.2 + - - +
213A GLY* 1.3 86.1 - - - +
215A LEU* 1.3 60.8 - - - +
216A VAL* 3.9 12.8 - - + -
225A LEU* 3.5 17.7 - - + -
227A GLY 3.9 0.2 - - - +
229A VAL* 4.8 2.1 - - - +
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Residues in contact with LEU 215 (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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147A CYS* 3.8 26.0 - - + -
148A GLU 3.5 2.9 - - - +
149A ILE* 3.6 21.8 - - + -
172A VAL* 4.2 13.7 - - + -
174A LEU* 4.1 21.3 - - + -
195A LEU* 4.9 4.7 - - + -
197A ALA* 4.7 2.9 - - + -
213A GLY 4.0 0.2 + - - -
214A PRO* 1.3 73.0 - - - +
216A VAL* 1.3 58.9 + - - +
217A CYS* 4.5 1.8 - - - -
225A LEU* 3.9 2.3 - - - +
226A THR* 3.1 31.8 + - + -
227A GLY* 2.9 29.8 + - - +
244A TYR* 3.8 40.6 - - + -
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Residues in contact with VAL 216 (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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14A TRP* 3.8 25.4 - - + +
132A ILE* 4.0 19.5 - - + -
147A CYS* 3.3 2.3 - - - +
148A GLU* 3.0 46.5 + - + +
214A PRO* 3.9 14.1 - - + -
215A LEU* 1.3 76.2 - - - +
217A CYS* 1.3 62.4 + - - +
218A SER 4.5 0.2 + - - -
223A MET* 3.8 30.6 - - + +
224A THR 3.3 22.7 - - - +
225A LEU* 4.4 2.2 - - + -
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Residues in contact with CYS 217 (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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141A PRO* 3.8 18.8 - - + -
145A THR* 4.6 4.0 - - + -
146A SER 4.8 0.2 - - - -
147A CYS* 2.2 46.4 - - - +
174A LEU* 4.4 4.5 - - - -
215A LEU* 4.5 3.8 - - - -
216A VAL* 1.3 76.1 - - - +
218A SER* 1.3 61.8 + - - +
219A LEU* 3.5 0.3 + - - +
224A THR* 2.9 35.4 + - - -
226A THR* 3.4 36.3 - - - +
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Residues in contact with SER 218 (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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145A THR* 4.8 9.1 - - - +
146A SER 5.0 4.8 + - - -
217A CYS* 1.3 73.1 - - - +
219A LEU* 1.3 60.7 + - - +
220A GLN 4.2 0.7 + - - -
221A GLY* 4.4 15.6 + - - -
222A ARG 3.6 8.0 - - - -
223A MET* 4.2 20.0 + - - +
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Residues in contact with LEU 219 (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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135A PRO* 6.2 0.2 - - + -
139A ASN* 3.7 30.3 - - - +
140A ASP* 4.0 14.4 - - - +
141A PRO* 3.8 32.8 - - + -
145A THR* 5.9 0.2 - - + -
217A CYS 4.4 2.5 - - - +
218A SER* 1.3 76.1 + - - +
220A GLN* 1.3 100.2 + - + +
221A GLY 3.0 0.7 - - - -
222A ARG* 2.9 25.6 + - - +
224A THR* 4.3 17.4 + - + +
226A THR* 5.6 0.9 - - - +
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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