Contacts of the strand formed by residues 221 - 227 (chain F) in PDB entry 6H25
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 GLN 221 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246E SER* 2.6 39.5 + - - +
247E LEU 3.6 3.8 - - - +
248E ASP* 2.1 47.7 + - - +
249E PRO* 4.5 0.9 - - - -
215F LEU* 3.3 5.5 - - - +
216F MET* 3.2 37.8 + - + +
219F LEU* 3.4 29.4 + - + +
220F ASN* 1.3 76.5 - - - +
222F VAL* 1.3 64.8 + - - +
223F ALA* 3.4 0.5 + - - -
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Residues in contact with VAL 222 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241E LYS* 4.0 2.3 + - + -
246E SER* 3.8 1.8 + - - -
247E LEU* 2.7 44.6 + - + +
248E ASP* 4.7 0.2 - - - +
249E PRO* 4.5 12.1 - - + -
252E ILE* 4.2 20.0 - - + -
213F VAL* 5.3 2.7 - - + -
214F ALA 3.9 10.1 - - - +
215F LEU* 3.9 5.2 - - + -
221F GLN* 1.3 70.9 - - - +
223F ALA* 1.3 62.9 + - - +
224F GLY* 3.8 16.2 - - - +
225F LEU* 4.1 26.5 - - + -
241F VAL* 5.4 2.9 - - + -
245F LEU* 4.0 28.9 - - + -
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Residues in contact with ALA 223 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241E LYS* 3.0 25.3 + - - +
246E SER* 5.2 0.2 - - - -
128F GLU 3.4 9.9 - - - +
129F ALA* 3.7 23.8 - - + +
132F PRO* 4.5 8.9 - - + +
133F ALA 6.2 0.2 - - - +
180F VAL* 4.9 5.8 - - + -
214F ALA* 2.8 22.6 + - + +
215F LEU* 4.6 4.0 - - - -
216F MET* 4.7 22.4 - - + -
221F GLN 3.4 1.6 + - - -
222F VAL* 1.3 73.1 - - - +
224F GLY* 1.3 55.3 + - - +
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Residues in contact with GLY 224 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241E LYS* 3.8 15.7 - - - -
128F GLU 5.6 0.2 - - - -
129F ALA* 4.6 11.5 - - - +
162F LEU* 5.6 1.4 - - - +
212F THR 4.0 0.7 - - - +
213F VAL* 3.7 2.3 - - - -
214F ALA* 3.2 28.7 + - - +
222F VAL* 3.6 5.3 - - - -
223F ALA* 1.3 81.4 - - - +
225F LEU* 1.3 61.2 + - - +
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Residues in contact with LEU 225 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226E LEU* 4.6 10.8 - - + -
239E MET* 3.8 41.3 - - + +
240E ARG* 3.4 4.7 - - - +
241E LYS* 3.1 34.6 + - + +
247E LEU* 5.8 1.1 - - + -
252E ILE* 4.3 27.8 - - + -
211F LEU* 5.8 4.3 - - + -
212F THR 3.4 4.5 - - - +
213F VAL* 3.8 23.3 - - + -
222F VAL* 4.1 19.3 - - + -
224F GLY* 1.3 74.2 - - - +
226F LEU* 1.3 60.8 + - - +
227F GLY 5.5 1.3 - - - +
241F VAL* 4.7 11.9 - - + -
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Residues in contact with LEU 226 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111E ARG* 3.5 36.8 - - - +
238E CYS* 5.7 1.3 - - + -
239E MET 3.6 9.9 - - - +
240E ARG* 4.1 24.7 - - + +
121F GLU* 3.4 23.1 - - - +
122F LEU* 4.9 6.5 - - + -
125F ALA* 4.1 27.4 - - + -
158F LEU* 5.2 8.5 - - + -
211F LEU* 5.3 0.9 - - - -
212F THR* 3.1 34.2 + - - +
225F LEU* 1.3 75.3 - - - +
227F GLY* 1.3 61.9 + - - +
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Residues in contact with GLY 227 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111E ARG* 4.3 1.6 - - - -
238E CYS* 3.2 22.8 - - - -
239E MET* 3.5 12.2 + - - +
210F GLY 3.2 14.4 - - - -
211F LEU* 3.7 13.8 - - - +
225F LEU* 5.5 1.2 - - - +
226F LEU* 1.3 78.3 - - - +
228F SER* 1.3 65.3 + - - -
237F TRP* 3.8 9.4 - - - -
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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