Contacts of the strand formed by residues 244 - 251 (chain A) in PDB entry 2H07
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 VAL 244 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A ALA* 3.0 7.0 - - + +
218A LEU* 3.9 12.3 - - + -
233A ALA* 4.1 15.9 - - + +
236A LEU* 3.7 33.9 - - + -
237A LEU* 4.6 7.6 - - + +
241A ALA* 5.4 0.7 - - + -
243A ARG* 1.3 72.2 - - - +
245A TYR* 1.3 74.0 + - - +
265A CYS* 3.2 40.9 + - - +
266A PHE* 3.5 7.1 - - + -
267A GLU* 3.2 20.2 + - - +
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Residues in contact with TYR 245 (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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154A TRP* 4.4 13.7 - + - -
158A ASN 4.6 6.5 + - - -
159A ILE* 3.7 32.1 - - + +
215A VAL* 3.4 32.5 - - + -
216A ALA 2.8 8.8 + - - +
217A ILE* 4.3 15.5 - - + -
218A LEU* 2.8 27.4 + - - +
243A ARG* 3.1 36.6 + - + -
244A VAL* 1.3 82.9 - - - +
246A ALA* 1.3 64.2 + - - +
247A ILE* 5.1 3.6 - - + -
266A PHE* 4.3 0.4 - - - -
267A GLU* 3.2 29.8 - - + +
268A ALA* 3.7 26.0 - - + +
270A VAL* 5.7 1.1 - - + -
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Residues in contact with ALA 246 (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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218A LEU* 3.2 7.2 - - + +
229A ILE* 4.2 16.6 - - + -
245A TYR* 1.3 76.9 - - - +
247A ILE* 1.3 63.1 + - - +
248A LEU* 4.1 3.4 - - + -
266A PHE* 3.5 31.6 - - + -
268A ALA 3.3 5.5 + - - -
269A VAL* 3.3 17.6 - - + +
270A VAL* 2.9 26.0 + - - +
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Residues in contact with ILE 247 (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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151A VAL* 3.6 31.6 - - + +
154A TRP* 4.4 16.4 - - + -
155A ILE* 3.6 33.7 - - + -
159A ILE* 5.6 0.2 - - + -
217A ILE* 3.8 20.6 - - + -
218A LEU 2.7 12.4 + - - +
219A VAL* 3.5 11.6 - - + +
220A ASP 3.1 25.1 + - - +
245A TYR* 5.1 2.9 - - + -
246A ALA* 1.3 77.9 - - - +
248A LEU* 1.3 68.3 + - - +
270A VAL* 3.4 24.9 - - + +
290A ILE* 5.6 1.3 - - + -
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Residues in contact with LEU 248 (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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218A LEU 5.7 0.2 - - - +
220A ASP* 3.3 32.8 - - + +
222A MET* 3.8 4.9 - - - +
223A ALA* 3.2 37.7 - - + +
226A CYS* 5.3 1.1 - - - -
229A ILE* 4.3 17.0 - - + -
246A ALA* 4.9 2.7 - - + -
247A ILE* 1.3 85.5 - - - +
249A THR* 1.3 60.8 + - - +
250A HIS 4.0 11.4 - - - +
253A PHE* 3.6 22.9 - - + -
269A VAL* 4.4 8.7 - - + -
270A VAL 2.8 6.7 + - - +
271A VAL* 3.0 38.8 - - + -
272A THR* 3.5 1.7 + - - +
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Residues in contact with THR 249 (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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127A MET* 4.3 4.3 - - - +
128A ASP* 3.4 31.7 + - + +
147A ALA* 4.3 4.7 - - - -
177A ARG* 6.2 0.4 - - - -
220A ASP 3.7 1.7 + - - +
221A ASP* 2.8 34.5 + - - +
248A LEU* 1.3 73.9 - - - +
250A HIS* 1.3 79.1 + - + +
251A GLY 3.9 0.9 + - - -
272A THR* 2.5 51.7 + - - +
274A THR* 3.2 1.7 + - - -
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Residues in contact with HIS 250 (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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90A PRO 3.2 16.8 - - - -
91A CYS* 3.8 29.6 - - - -
92A PHE 5.6 0.6 + - - -
127A MET 3.0 29.1 + - - -
128A ASP* 3.2 15.0 + - - +
221A ASP* 3.0 23.4 + - + +
222A MET* 3.1 40.7 - - + +
223A ALA 3.3 5.9 + - - -
248A LEU* 4.0 5.2 - - - +
249A THR* 1.3 91.2 + - + +
251A GLY* 1.3 60.4 + - - +
252A ILE* 3.6 2.0 + - + -
274A THR* 3.1 27.6 + - + +
275A ILE* 4.5 3.1 - - + -
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Residues in contact with GLY 251 (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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223A ALA 4.1 2.9 - - - -
248A LEU* 4.9 0.7 - - - -
249A THR 3.9 3.6 + - - -
250A HIS* 1.3 69.0 - - - +
252A ILE* 1.3 57.8 + - - -
253A PHE* 2.9 33.7 + - - +
271A VAL* 4.2 8.2 - - - +
272A THR 5.3 0.6 + - - -
274A THR* 4.7 1.0 + - - -
275A ILE* 3.9 15.4 - - - +
276A PRO 5.2 0.2 - - - +
277A GLN* 3.0 29.8 + - - +
280A LYS* 5.5 0.7 - - - +
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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