Contacts of the strand formed by residues 199 - 208 (chain A) in PDB entry 1QYO
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 199 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A TYR* 2.7 40.9 + + - -
78A MET* 3.9 11.0 - - + -
81A HIS* 3.7 8.3 - - + +
151A TYR* 3.7 4.0 - - - +
152A ILE* 2.8 52.5 + - + +
196A PRO* 3.6 23.9 - - + +
197A ASP 3.0 18.6 + - - -
198A ASN* 1.3 74.5 - - - +
200A TYR* 1.3 77.9 + - - +
201A LEU* 4.6 0.2 - - + -
226A ALA* 4.3 1.6 - - + -
227A ALA 3.3 11.9 - - - +
228A GLY* 4.7 5.2 - - - -
229A ILE* 3.8 15.5 - - + -
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Residues in contact with TYR 200 (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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149A ASN* 3.5 35.2 - - + -
150A VAL 3.1 14.6 - - - +
151A TYR* 3.8 30.5 - + + -
199A HIS* 1.3 80.8 - - - +
201A LEU* 1.3 64.6 + - - +
202A SER* 4.0 12.1 - - - -
226A ALA* 3.3 4.0 - - - -
227A ALA* 2.9 57.9 + - + +
228A GLY* 3.6 21.7 + - - -
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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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69A GLN* 3.7 32.3 - - + +
72A SER* 3.6 22.7 - - - +
74A TYR* 3.5 37.2 - - + +
84A PHE* 4.0 13.2 - - + -
149A ASN* 3.4 2.1 - - - -
150A VAL* 2.9 37.9 + - + +
152A ILE* 3.8 13.7 - - + -
199A HIS* 4.5 0.7 - - - +
200A TYR* 1.3 74.4 - - - +
202A SER* 1.3 62.1 + - - +
203A THR* 3.2 7.8 + - - +
224A VAL* 3.7 13.0 - - + -
225A THR 3.5 2.2 - - - -
226A ALA* 4.0 13.7 - - + +
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Residues in contact with SER 202 (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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148A HIS 4.8 0.5 + - - -
149A ASN* 3.5 20.4 + - - -
200A TYR* 4.0 12.9 - - - -
201A LEU* 1.3 67.7 - - - +
203A THR* 1.3 59.5 + - - +
204A GLN* 4.9 15.2 + - - +
223A PHE 3.5 2.8 - - - +
224A VAL* 3.3 3.5 - - - -
225A THR* 2.7 43.7 + - - -
227A ALA* 5.5 2.5 - - - -
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Residues in contact with THR 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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66A GLY* 6.3 0.4 - - - -
69A GLN* 5.5 0.5 + - - -
147A SER* 3.4 5.9 - - - -
148A HIS* 2.8 65.4 + - + +
150A VAL* 3.8 12.0 - - + +
201A LEU* 3.2 12.5 + - - +
202A SER* 1.3 73.5 + - - +
204A GLN* 1.3 63.9 + - - +
205A SER* 4.2 2.6 + - - +
222A GLU* 3.7 33.2 - - + +
223A PHE 3.4 1.8 - - - -
224A VAL* 3.5 19.6 - - + +
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Residues in contact with GLN 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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147A SER* 4.0 19.2 - - - -
202A SER* 4.9 14.2 + - - +
203A THR* 1.3 78.0 - - - +
205A SER* 1.3 61.6 + - - +
221A LEU 3.9 0.9 - - - +
222A GLU* 3.3 4.5 - - - -
223A PHE* 2.9 63.3 + - + +
225A THR* 5.5 4.4 + - - -
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Residues in contact with SER 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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61A VAL* 3.9 6.3 - - - +
145A TYR* 3.7 54.4 + - - +
146A ASN 5.7 0.2 - - - -
147A SER* 5.3 2.6 - - - +
148A HIS* 4.8 1.0 - - - -
203A THR* 4.2 6.1 + - - +
204A GLN* 1.3 73.6 - - - +
206A ALA* 1.3 59.5 + - - +
207A LEU* 4.6 1.1 - - - -
220A LEU* 3.9 10.1 - - - -
221A LEU 3.6 3.6 - - - -
222A GLU* 2.9 30.2 + - - -
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Residues in contact with ALA 206 (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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205A SER* 1.3 74.6 - - - +
207A LEU* 1.3 62.4 + - - +
208A SER* 5.1 0.9 + - - -
219A VAL 3.6 1.2 - - - +
220A LEU* 3.5 5.2 - - - +
221A LEU* 2.8 56.6 + - + +
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Residues in contact with LEU 207 (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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58A PRO* 3.8 33.7 - - + -
61A VAL* 3.8 16.6 - - + -
143A TYR* 3.8 33.8 - - + +
144A ASN* 3.8 21.6 - - - +
145A TYR* 4.5 7.5 - - + +
205A SER* 4.6 5.4 - - - -
206A ALA* 1.3 77.1 - - - +
208A SER* 1.3 63.3 + - - +
218A MET* 4.0 18.6 - - + -
219A VAL 3.5 2.9 - - - +
220A LEU* 3.7 26.7 - - + -
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Residues in contact with SER 208 (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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143A TYR* 2.7 27.1 + - - -
206A ALA 5.1 1.0 + - - -
207A LEU* 1.3 75.7 - - - +
209A LYS* 1.3 66.9 + - - +
219A VAL* 3.0 43.4 + - - +
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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