Contacts of the strand formed by residues 257 - 264 (chain A) in PDB entry 4HBT
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 LEU 257 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LEU* 4.0 14.1 - - + -
50A ILE 3.3 6.3 - - - +
51A ASN* 3.5 41.7 - - + +
195A LEU* 5.1 0.2 - - - -
229A TRP* 4.2 6.7 - - + -
248A VAL* 3.5 5.7 - - - +
249A ILE* 2.8 45.6 + - + +
251A PRO* 4.0 23.3 - - + -
255A ALA 4.3 3.6 - - - +
256A PRO* 1.3 76.8 - - - +
258A ILE* 1.3 65.6 + - - +
259A LEU 4.3 0.2 - - - -
285A THR* 4.0 18.4 - - + -
288A LEU* 3.9 24.7 - - + -
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Residues in contact with ILE 258 (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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48A ALA 3.7 0.9 - - - +
49A LEU* 3.3 6.3 - - - +
50A ILE* 2.8 43.0 + - + -
52A THR* 5.4 0.9 - - + -
187A ALA* 3.4 36.3 - - + +
190A LEU* 4.1 12.3 - - + -
191A ARG* 3.7 28.0 - - + +
194A THR* 3.6 23.8 - - - +
195A LEU* 4.0 10.5 - - + -
247A ALA 3.4 5.6 - - - +
248A VAL* 3.7 24.5 - - + -
257A LEU* 1.3 74.7 - - - +
259A LEU* 1.3 63.5 + - - +
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Residues in contact with LEU 259 (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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47A VAL* 3.9 11.4 - - + -
48A ALA 3.4 9.6 - - - +
49A LEU* 4.0 11.2 - - + -
221A ILE* 3.6 25.8 - - + +
225A LEU* 5.4 0.2 - - + -
246A ILE* 3.4 2.3 - - - -
247A ALA 2.8 37.4 + - - +
249A ILE* 3.9 19.7 - - + -
257A LEU 4.3 0.4 - - - -
258A ILE* 1.3 75.2 - - - +
260A VAL* 1.3 76.0 + - - +
261A THR* 3.9 5.4 - - + -
281A ALA* 3.7 35.9 - - + +
284A VAL* 3.9 24.0 - - + -
285A THR* 5.1 2.5 - - + -
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Residues in contact with VAL 260 (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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47A VAL* 3.3 6.4 - - - -
48A ALA 2.9 32.8 + - - +
183A PRO* 3.9 28.3 - - + +
186A MET* 3.9 5.4 - - + +
187A ALA* 3.5 35.4 - - + +
190A LEU* 5.4 0.9 - - + -
245A ASP 3.7 2.9 - - - -
246A ILE* 3.8 18.4 - - + -
258A ILE* 5.0 1.8 - - + -
259A LEU* 1.3 77.7 - - - +
261A THR* 1.3 66.8 + - - +
262A TYR* 3.8 34.5 - - + -
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Residues in contact with THR 261 (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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45A LEU* 5.2 1.3 - - - -
46A GLY 3.4 4.0 - - - -
47A VAL* 4.5 5.4 - - + -
221A ILE* 3.5 16.9 - - + +
244A ASN* 3.4 3.1 - - - -
245A ASP* 2.9 36.7 + - - +
259A LEU* 3.9 26.4 - - + -
260A VAL* 1.3 77.6 - - - +
262A TYR* 1.3 61.9 + - - +
277A LEU* 3.6 28.8 - - - +
280A ALA* 4.0 25.1 - - + -
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Residues in contact with TYR 262 (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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44A ARG 3.9 0.2 - - - +
45A LEU* 3.5 4.9 - - - +
46A GLY* 2.8 35.4 + - - +
66A PHE* 3.7 46.7 - + + -
68A MET* 3.8 8.5 - - + +
71A THR* 2.8 28.2 + - - -
181A THR* 3.9 20.6 - - + -
182A SER 4.6 3.4 - - - -
183A PRO* 4.2 7.2 - - + -
186A MET* 3.5 25.1 - - + +
244A ASN* 3.3 26.9 - - + +
246A ILE* 3.7 17.3 - - + -
260A VAL* 3.8 18.6 - - + -
261A THR* 1.3 81.3 - - - +
263A PHE* 1.3 63.3 + - - +
277A LEU* 4.5 0.2 - - - -
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Residues in contact with PHE 263 (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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41A SER* 3.1 40.2 - - - -
43A GLY* 3.7 17.5 - - - -
44A ARG 3.4 18.8 - - - -
45A LEU* 4.1 8.7 - - + -
66A PHE* 4.4 1.7 - - - -
241A GLY 4.3 3.4 - - - -
242A THR* 3.2 6.3 - - - +
243A THR* 2.8 44.5 + - - +
244A ASN* 3.2 3.0 + - - -
262A TYR* 1.3 75.1 - - - +
264A THR* 1.3 61.0 + - - +
265A GLN* 3.4 40.4 - - + -
273A ARG* 3.8 24.0 - - + -
276A VAL* 3.9 17.5 - - + -
277A LEU* 3.8 12.1 - - + -
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Residues in contact with THR 264 (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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43A GLY* 3.3 2.8 - - - -
44A ARG* 2.8 71.9 + - + +
66A PHE* 4.2 8.3 - - + -
67A ALA 6.2 1.3 - - - +
172A ALA* 4.6 3.8 + - - +
174A PRO* 5.8 4.1 - - + +
240A TYR* 3.5 13.7 + - - +
241A GLY 4.4 0.2 - - - -
242A THR* 2.7 26.5 + - - +
263A PHE* 1.3 77.2 - - - +
265A GLN* 1.3 67.4 + - - +
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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