Contacts of the strand formed by residues 217 - 227 (chain A) in PDB entry 1OXD
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 HIS 217 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A LYS* 4.2 3.4 - - - -
46A PHE 3.0 15.9 - - - +
47A ILE* 3.4 15.5 - - + -
57A TRP* 3.4 10.5 + - - -
209A LYS* 2.7 53.5 + - + +
210A ASP* 2.8 44.3 + - + +
213A GLU* 3.4 30.8 - - + +
215A ARG 2.8 18.1 + - - +
216A ASP* 1.3 78.9 + - - +
218A MET* 1.3 63.9 + - - +
219A VAL* 4.1 11.2 - - + -
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Residues in contact with MET 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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45A LYS* 3.4 1.4 - - - -
46A PHE* 2.8 63.3 + - + -
57A TRP* 3.7 41.5 - - + +
61A VAL* 3.9 22.9 - - + -
64A LEU* 3.9 12.6 - - + -
143A TYR* 3.3 17.5 - - + +
207A LEU* 3.7 28.0 - - + -
208A SER 4.1 0.9 - - - -
217A HIS* 1.3 76.6 - - - +
219A VAL* 1.3 74.2 + - - +
220A LEU* 4.5 8.1 - - + +
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Residues in contact with VAL 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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44A LEU 3.5 9.9 - - - +
45A LYS* 4.2 14.4 - - + -
206A ALA 3.6 0.3 - - - +
207A LEU* 3.4 5.5 - - - -
208A SER* 2.9 51.9 + - - +
209A LYS 4.1 1.1 - - - -
210A ASP* 3.9 33.2 - - + +
217A HIS* 4.1 7.6 - - + -
218A MET* 1.3 77.1 - - - +
220A LEU* 1.3 66.8 + - - +
221A LEU* 6.2 1.1 - - + -
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Residues in contact with LEU 220 (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 LEU 3.9 0.9 - - - +
43A THR* 3.5 3.6 - - - -
44A LEU* 2.8 42.8 + - + +
46A PHE* 4.1 17.0 - - + -
61A VAL* 4.2 11.7 - - + -
64A LEU* 6.1 0.2 - - + -
66A CRF 3.5 25.1 - - + +
205A SER* 4.0 5.2 - - - -
206A ALA 3.4 14.8 - - - +
207A LEU* 3.7 25.8 - - + -
218A MET* 4.5 10.1 - - + -
219A VAL* 1.3 80.3 - - - +
221A LEU* 1.3 60.1 + - - +
222A GLU* 3.2 39.9 - - + +
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Residues in contact with LEU 221 (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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41A LYS* 4.3 7.2 - - - -
42A LEU 3.5 6.3 - - - +
43A THR* 3.5 28.3 - - + -
204A GLN 3.7 0.9 - - - +
205A SER* 3.6 0.9 - - - -
206A ALA* 2.9 47.5 + - + +
219A VAL* 6.2 1.1 - - + -
220A LEU* 1.3 72.9 - - - +
222A GLU* 1.3 61.5 + - - +
223A PHE* 3.8 35.6 - - + -
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Residues in contact with GLU 222 (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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40A GLY 4.1 0.7 - - - -
41A LYS* 3.5 3.8 - - - +
42A LEU* 2.9 56.4 + - + +
44A LEU* 5.3 0.8 - - + +
61A VAL* 3.4 3.6 - - - +
66A CRF 2.9 48.6 + - - +
203A THR* 4.3 7.3 - - + +
204A GLN 3.1 5.2 - - - +
205A SER* 2.8 31.7 + - - +
220A LEU* 3.2 22.5 - - + +
221A LEU* 1.3 79.0 - - - +
223A PHE* 1.3 69.4 + - - +
224A VAL* 4.8 1.8 - - + +
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Residues in contact with PHE 223 (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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39A TYR* 4.3 9.4 - - + +
40A GLY 3.1 6.1 - - - +
41A LYS* 3.5 39.9 - - + -
202A SER 3.7 1.4 - - - +
203A THR* 3.3 1.9 - - - -
204A GLN* 2.8 64.0 + - + +
221A LEU* 3.8 39.9 - - + -
222A GLU* 1.3 77.2 - - - +
224A VAL* 1.3 62.5 + - - +
225A THR* 5.2 2.2 - - - +
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Residues in contact with VAL 224 (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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40A GLY* 2.8 21.4 + - - +
42A LEU* 4.8 12.3 - - + -
66A CRF 6.0 0.7 - - + -
69A GLN* 6.1 1.8 - - + -
71A PHE 5.2 0.7 - - - +
72A SER* 3.4 31.4 - - - +
73A ARG* 2.9 21.5 + - - +
201A LEU* 4.1 16.4 - - + -
202A SER 3.3 4.9 - - - +
203A THR* 3.0 38.1 - - + +
222A GLU* 4.8 6.1 - - + +
223A PHE* 1.3 79.7 - - - +
225A THR* 1.3 66.9 + - - +
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Residues in contact with THR 225 (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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39A TYR 5.6 1.2 + - - -
73A ARG* 3.5 46.6 + - - +
75A PRO* 4.8 3.4 - - + -
201A LEU* 4.4 1.8 - - - -
202A SER* 2.8 43.8 + - - +
204A GLN* 5.7 2.6 + - - -
223A PHE* 5.2 1.7 - - - +
224A VAL* 1.3 80.4 + - - +
226A ALA* 1.3 76.1 + - - +
227A ALA* 4.8 2.5 - - + +
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Residues in contact with ALA 226 (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 ARG 2.9 11.5 + - - +
74A TYR* 3.6 43.7 - - + -
75A PRO* 3.3 24.0 - - + +
78A MET* 4.0 6.3 - - + -
199A HIS* 4.3 0.2 - - + -
200A TYR 3.4 7.4 - - - +
201A LEU* 3.8 14.5 - - + +
225A THR* 1.3 79.9 - - - +
227A ALA* 1.3 63.7 + - - +
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Residues in contact with ALA 227 (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 PRO* 5.4 0.9 - - - -
78A MET* 3.8 10.9 - - - +
199A HIS* 3.3 7.6 - - - +
200A TYR* 2.9 55.7 + - + +
202A SER* 5.7 1.6 - - - -
225A THR* 4.8 4.3 - - + +
226A ALA* 1.3 76.6 - - - +
228A GLY* 1.3 62.8 + - - +
229A ILE 3.5 2.5 - - - -
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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