Contacts of the strand formed by residues 200 - 205 (chain A) in PDB entry 1OWK
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 200 (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* 3.8 26.2 - - + +
15A PHE* 3.9 24.0 - - + -
32A GLY 3.9 4.3 - - - +
33A SER* 3.4 24.2 - - - +
135A GLU 3.6 0.7 - - - +
136A ILE* 3.3 24.1 - - - +
137A THR* 3.6 21.7 + - - +
199A GLY* 1.3 85.8 - - - +
201A LEU* 1.3 59.5 + - - +
202A VAL* 3.8 6.3 - - + -
211A LEU* 4.0 11.2 - - + -
213A GLY 4.2 0.2 - - - +
215A VAL* 4.9 1.7 - - - +
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Residues in contact with LEU 201 (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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134A CYS* 4.3 13.7 - - + -
135A GLU 3.3 4.9 - - - +
136A ILE* 3.2 25.6 - - + -
158A VAL* 4.2 14.1 - - + -
160A LEU* 4.3 21.1 - - + -
181A LEU* 5.1 4.7 - - + -
183A ALA* 4.7 1.1 - - + -
200A PRO* 1.3 72.7 - - - +
202A VAL* 1.3 59.4 + - - +
203A CYS* 3.9 4.3 + - - -
210A THR 3.9 0.2 - - - +
211A LEU* 4.1 2.0 - - - +
212A THR* 3.3 24.7 + - - -
213A GLY* 3.2 32.7 + - - +
230A TYR* 3.6 41.5 - - + -
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Residues in contact with VAL 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A TRP* 3.6 33.7 - - + +
119A ILE* 4.4 7.0 - - + -
134A CYS* 3.0 19.3 - - - +
135A GLU* 2.9 33.5 + - + +
200A PRO* 4.2 10.1 - - + -
201A LEU* 1.3 75.0 - - - +
203A CYS* 1.3 62.4 + - - +
204A SER 4.3 0.3 + - - -
209A MET* 3.7 44.9 - - + -
210A THR 3.4 13.2 - - - +
211A LEU* 4.8 5.8 - - + -
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Residues in contact with CYS 203 (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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128A PRO* 4.1 14.6 - - + -
132A THR* 5.0 1.6 - - + -
134A CYS* 2.0 48.5 - - - +
160A LEU* 4.1 19.3 - - - -
201A LEU* 4.6 5.4 - - - -
202A VAL* 1.3 75.6 - - - +
204A SER* 1.3 60.9 + - - +
205A LEU* 3.0 5.7 + - + +
210A THR* 2.8 36.6 + - - +
212A THR* 3.8 26.7 - - - +
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Residues in contact with SER 204 (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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128A PRO* 5.8 1.1 - - - +
132A THR* 5.3 8.3 - - - +
133A SER 4.9 5.8 + - - -
202A VAL* 4.3 1.2 + - - +
203A CYS* 1.3 70.7 - - - +
205A LEU* 1.3 59.2 + - - +
206A GLN 3.8 1.7 + - - -
207A GLY* 3.8 22.5 + - - -
208A ARG 3.9 5.1 - - - -
209A MET* 4.2 18.5 + - - +
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Residues in contact with LEU 205 (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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122A PRO* 5.5 2.7 - - + -
123A SER* 5.7 1.8 - - - +
126A ASN* 3.1 37.5 - - + +
127A ASP 4.7 0.2 - - - -
128A PRO* 4.1 37.5 - - + -
203A CYS* 3.0 7.2 + - + +
204A SER* 1.3 69.4 - - - +
206A GLN* 1.3 99.6 + - + +
207A GLY 3.2 1.1 - - - -
208A ARG* 3.1 19.0 + - - +
210A THR* 3.5 28.6 + - + +
212A THR* 5.5 0.2 - - - +
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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