Contacts of the strand formed by residues 224 - 230 (chain E) 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 ALA 224 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204E CYS* 4.6 0.7 - - - -
205E LYS* 3.2 20.4 + - + +
222E SER* 3.2 15.1 + - - -
223E LEU* 1.3 78.1 - - - +
225E SER* 1.3 64.5 + - - +
241E LYS* 4.4 11.4 - - + +
242E VAL 3.7 5.6 - - - -
243E GLY* 4.3 1.3 - - - -
245E GLY 3.9 14.4 - - - +
246E SER 3.6 25.4 - - - +
247E LEU* 4.8 12.1 - - + -
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Residues in contact with SER 225 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202E THR* 5.9 3.4 - - - -
203E LEU 4.0 6.1 - - - -
204E CYS* 4.0 22.2 - - - -
205E LYS* 4.5 0.9 - - - +
224E ALA* 1.3 79.1 - - - +
226E LEU* 1.3 63.5 + - - +
241E LYS* 3.6 8.0 - - - +
242E VAL* 2.3 68.8 + - - +
247E LEU* 5.2 4.4 - - - +
255E MET* 6.3 0.2 - - - -
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Residues in contact with LEU 226 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201E VAL 4.2 0.3 - - - +
202E THR* 3.5 4.7 - - - -
203E LEU* 2.9 43.6 + - + +
225E SER* 1.3 74.1 - - - +
227E LEU* 1.3 63.4 + - - +
228E VAL* 3.8 24.7 - - + -
239E MET* 4.9 4.5 - - + -
240E ARG 3.6 19.5 - - - +
241E LYS* 4.9 1.6 - - - +
247E LEU* 4.9 10.8 - - + -
252E ILE* 4.2 20.6 - - + +
255E MET* 3.8 43.9 - - + +
256E MET* 4.6 1.8 - - + +
225F LEU* 4.6 21.1 - - + -
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Residues in contact with LEU 227 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108E THR* 5.7 6.3 - - + -
112E ILE* 5.3 4.9 - - + -
149E PHE* 4.2 22.4 - - + -
200E ILE* 3.7 37.7 - - + -
201E VAL 4.0 0.9 - - - -
202E THR* 3.7 28.3 - - + -
226E LEU* 1.3 74.5 - - - +
228E VAL* 1.3 61.9 + - - +
229E SER 5.3 0.4 - - - +
238E CYS* 3.8 6.8 - - - +
239E MET* 3.2 7.3 - - - -
240E ARG* 2.8 55.6 + - + +
242E VAL* 4.7 13.2 - - + -
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Residues in contact with VAL 228 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200E ILE* 4.6 2.2 - - - -
201E VAL* 2.9 40.5 + - + +
203E LEU* 5.0 10.5 - - + -
226E LEU* 3.8 29.6 - - + -
227E LEU* 1.3 77.3 - - - +
229E SER* 1.3 61.7 + - - +
230E VAL* 3.8 22.5 + - + +
236E VAL* 4.1 20.0 - - + -
238E CYS 4.3 2.0 - - - -
239E MET* 4.0 17.9 - - + -
256E MET* 5.1 15.5 - - + +
259E GLY* 5.2 6.5 - - - -
260E LYS 5.6 0.2 - - - +
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Residues in contact with SER 229 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112E ILE* 3.9 22.5 - - - +
198E PRO* 4.7 2.5 - - - -
199E CYS 3.3 10.5 - - - -
200E ILE* 4.1 9.6 - - - +
227E LEU* 5.3 0.6 - - - +
228E VAL* 1.3 72.9 - - - +
230E VAL* 1.3 60.6 + - - +
236E VAL* 3.6 9.0 - - - +
237E THR* 2.3 60.1 + - - -
238E CYS 3.1 11.8 + - - -
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Residues in contact with VAL 230 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198E PRO* 4.0 2.2 - - - -
199E CYS* 2.9 31.4 + - - +
201E VAL* 5.2 3.6 - - + -
228E VAL* 3.8 23.3 - - + +
229E SER* 1.3 77.5 - - - +
231E THR* 1.3 74.0 + - - +
232E SER 5.7 0.2 - - - +
233E LYS 6.2 0.2 - - - -
234E GLY* 5.3 6.3 - - - -
235E VAL 3.7 7.6 - - - +
236E VAL* 4.8 7.2 - - + +
259E GLY 3.7 22.0 - - - +
260E LYS* 4.1 19.5 - - + +
263E GLY* 4.0 22.9 - - - -
264E LYS* 4.8 1.8 - - + +
267E HIS* 3.3 7.3 + - - -
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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