Contacts of the strand formed by residues 207 - 210 (chain N) in PDB entry 2I2X
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 PHE 207 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129N HIS* 3.8 13.5 - + - -
178N LEU* 3.1 30.5 - - + -
179N THR 3.7 24.7 - - - -
180N GLY* 3.8 4.9 - - - -
191N PHE* 3.8 28.7 - + + -
194N VAL* 3.4 28.9 - - + -
195N ASN* 3.8 23.6 - - + -
198N LEU* 5.2 2.9 - - + -
205N ILE 3.6 2.4 + - - +
206N PRO* 1.3 72.5 - - - +
208N ALA* 1.3 63.1 + - - +
209N CYS* 3.1 28.9 + - - -
222N PHE* 6.3 1.8 - + - -
224N LEU* 3.7 26.2 + - + +
225N GLY* 4.2 1.0 - - - -
226N VAL* 3.6 12.3 + - - +
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Residues in contact with ALA 208 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177N MET* 4.3 12.8 - - + -
178N LEU 2.9 9.1 + - - +
179N THR* 3.2 2.6 - - + -
180N GLY 3.0 19.6 + - - -
206N PRO 3.7 2.0 - - - -
207N PHE* 1.3 70.6 - - - +
209N CYS* 1.3 58.7 + - - +
226N VAL* 3.5 15.8 - - + +
228N GLY* 5.5 2.9 - - - +
234N ALA* 5.7 0.2 - - - -
237N ILE* 4.2 25.6 - - + -
500N B13 2.8 33.4 + - + +
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Residues in contact with CYS 209 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180N GLY 3.6 3.6 - - - -
191N PHE* 3.2 37.0 - - + -
207N PHE* 3.1 41.1 - - - -
208N ALA* 1.3 74.1 - - - +
210N GLY* 1.3 55.5 + - - +
214N VAL* 4.2 1.8 - - + -
219N VAL* 3.5 25.6 - - + -
222N PHE* 5.7 2.5 - - - -
225N GLY* 4.9 2.7 - - - -
226N VAL 2.7 11.9 + - - +
227N TYR* 3.5 6.4 - - - -
228N GLY 2.8 30.6 + - - +
500N B13 4.2 3.4 - - - -
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Residues in contact with GLY 210 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180N GLY 3.0 8.4 + - - +
181N THR* 3.2 5.7 - - - -
182N ALA 3.2 22.0 + - - +
191N PHE* 4.0 3.1 - - - -
209N CYS* 1.3 75.5 - - - +
211N GLY* 1.3 59.8 + - - -
214N VAL* 4.0 10.4 - - - +
228N GLY 3.3 14.1 - - - -
500N B13 3.4 20.1 - - - -
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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