Contacts of the strand formed by residues 207 - 212 (chain A) in PDB entry 1ORZ
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 ILE 207 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A ILE* 4.4 24.8 - - + +
21A ILE* 3.8 14.4 + - - +
185A LEU* 3.8 17.7 - - + -
198A ILE* 3.3 30.3 - - + -
199A ALA 3.5 7.9 - - - +
200A TYR* 4.6 3.4 - - + +
205A GLY 3.9 0.4 + - - +
206A THR* 1.4 78.0 - - - +
208A HIS* 1.3 67.2 + - - +
458A ILE* 3.9 32.5 - - + -
461A LEU* 4.1 11.2 - - + -
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Residues in contact with HIS 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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20A ILE* 5.8 1.3 - - - -
21A ILE* 3.2 39.3 - - + -
22A ASP 3.2 0.4 - - - -
23A HIS* 2.7 55.9 + + + -
182A TYR* 6.2 3.1 - - + -
198A ILE* 3.1 6.4 - - - +
199A ALA 2.8 34.1 + - - +
206A THR* 4.4 3.8 + - - +
207A ILE* 1.3 76.9 - - - +
209A ARG* 1.3 78.3 + - - +
210A PHE* 3.1 43.3 - + + -
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Residues in contact with ARG 209 (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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18A TYR* 4.5 13.7 - - - +
20A ILE* 2.9 55.4 + - + +
21A ILE 3.1 8.8 + - - +
22A ASP* 2.5 47.1 + - - +
23A HIS 3.2 1.0 + - - -
188A LEU* 3.6 19.3 - - + -
197A VAL 3.5 6.3 - - - +
198A ILE* 3.4 19.3 - - + -
208A HIS* 1.3 87.3 + - - +
210A PHE* 1.3 56.8 + - - +
211A ARG* 4.3 6.1 - - - +
449A LEU* 2.9 35.6 + - - +
450A PRO 5.0 1.4 + - - -
451A SER* 5.3 5.1 - - - +
454A GLY* 4.2 8.8 - - - -
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Residues in contact with PHE 210 (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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23A HIS* 3.6 4.9 - - - +
25A TYR* 4.2 16.2 - + - -
28A VAL* 3.9 22.3 - - + +
51A ALA* 4.9 3.6 - - + -
53A ILE* 4.4 8.5 - - + -
179A PHE* 3.7 45.5 - + - -
182A TYR* 4.6 10.5 - + - -
195A VAL 4.3 0.2 - - - +
196A GLY* 3.0 4.7 - - - -
197A VAL* 2.6 50.4 + - + +
199A ALA* 3.4 33.0 - - + -
208A HIS* 3.1 39.5 - + + -
209A ARG* 1.3 71.7 - - - +
211A ARG* 1.3 59.2 + - - +
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Residues in contact with ARG 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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22A ASP* 3.2 40.9 + - - +
23A HIS 3.1 9.4 + - - +
24A GLU* 3.5 16.4 - - + +
25A TYR* 3.1 25.1 + - - +
28A VAL* 4.5 0.5 - - - +
188A LEU* 6.6 0.2 - - - -
195A VAL* 4.1 14.2 - - + +
196A GLY* 4.0 3.6 - - - -
209A ARG* 4.3 7.3 - - + +
210A PHE* 1.3 72.9 - - - +
212A ALA* 1.3 70.5 + - - +
213A HIS* 6.2 2.7 - - + +
447A LYS 5.5 0.4 + - - -
448A PRO* 3.8 20.5 - - - +
449A LEU* 3.0 56.7 + - + +
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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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24A GLU* 5.3 0.9 - - - -
25A TYR 3.3 13.2 - - - +
27A CYS* 3.9 0.9 - - - -
28A VAL* 3.4 25.6 - - + +
194A VAL 4.5 0.2 - - - +
195A VAL* 3.5 13.2 - - - +
196A GLY* 3.4 23.9 + - - -
211A ARG* 1.3 84.6 - - - +
213A HIS* 1.3 64.1 + - - +
214A LYS* 3.1 23.6 + - - +
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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