Contacts of the strand formed by residues 272 - 282 (chain A) in PDB entry 4H3T
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 272 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267A GLU 3.8 0.2 - - - +
268A ARG* 3.5 2.5 - - - -
269A ARG* 2.8 41.6 + - + +
271A ASP* 1.4 84.7 + - - +
273A ILE* 1.3 62.6 - - - +
274A VAL* 3.9 14.7 + - + -
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Residues in contact with ILE 273 (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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5A MSE 4.0 37.7 - - + -
6A HIS 3.8 22.9 - - - +
7A PHE* 5.9 1.1 - - + -
102A PHE* 3.6 27.6 - - + -
154A PRO* 3.2 25.9 - - + +
266A PRO* 4.0 7.9 - - + -
267A GLU 3.6 3.8 - - - +
268A ARG* 3.5 40.4 - - - +
271A ASP 4.0 1.0 + - - +
272A ALA* 1.3 72.3 - - - +
274A VAL* 1.3 68.3 + - - +
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Residues in contact with VAL 274 (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 ALA* 3.9 19.3 - - + -
152A LEU 3.4 14.6 - - - +
153A SER* 5.1 2.7 - - - -
154A PRO* 4.7 0.9 - - - -
266A PRO* 3.3 5.5 - - - +
267A GLU* 2.8 39.5 + - + +
269A ARG* 3.6 38.6 - - + +
272A ALA* 4.5 14.4 - - + +
273A ILE* 1.3 80.4 - - - +
275A VAL* 1.3 63.2 + - - +
276A PRO* 3.6 4.9 - - + +
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Residues in contact with VAL 275 (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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102A PHE* 3.8 31.6 - - + -
125A ALA* 3.1 17.8 - - + +
151A ALA* 4.1 1.3 - - - -
152A LEU* 2.8 36.2 + - + +
153A SER 4.6 2.9 - - - +
154A PRO* 4.6 1.3 - - + -
157A ALA* 3.9 23.3 - - + -
264A LEU* 3.9 27.1 - - + -
265A PHE 4.2 5.4 - - - +
266A PRO* 4.5 1.6 - - + -
274A VAL* 1.3 78.9 - - - +
276A PRO* 1.3 59.1 - - - +
277A ARG 3.5 20.6 - - - +
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Residues in contact with PRO 276 (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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124A THR* 3.3 11.6 - - - +
125A ALA* 2.8 20.5 + - + -
149A GLU 5.9 1.1 - - - +
151A ALA* 3.9 13.0 - - + -
265A PHE 3.3 18.6 - - - +
267A GLU* 3.7 28.5 - - + +
269A ARG* 3.6 19.3 - - - +
274A VAL* 3.6 11.4 - - + +
275A VAL* 1.3 85.5 - - - +
277A ARG* 1.3 69.7 + - + +
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Residues in contact with ARG 277 (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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122A VAL* 3.8 28.8 - - + +
123A LYS 3.3 12.3 - - - +
124A THR* 4.7 6.7 - - + -
125A ALA* 3.7 2.9 - - - +
265A PHE* 3.0 59.5 + - + +
275A VAL* 3.5 8.6 - - - +
276A PRO* 1.3 95.1 - - + +
278A VAL* 1.4 65.0 + - - +
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Residues in contact with VAL 278 (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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122A VAL* 3.6 1.0 - - - +
123A LYS* 2.8 35.1 + - + +
124A THR 3.8 8.7 - - - +
125A ALA* 4.0 8.7 - - + -
127A SER* 3.3 26.9 - - - +
128A LEU* 4.3 11.4 - - + -
262A ILE* 3.8 22.7 - - + -
263A ARG 3.3 15.7 - - - +
264A LEU* 3.9 16.4 - - + -
265A PHE* 3.9 6.0 - - - -
277A ARG* 1.4 75.5 - - - +
279A LEU* 1.3 61.6 + - - +
280A ILE* 3.8 17.0 + - + -
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Residues in contact with LEU 279 (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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114A LEU* 3.8 22.4 - - + +
115A GLU* 3.5 37.2 - - - -
116A PRO* 3.5 10.5 - - + -
121A GLY* 3.7 18.2 - - - +
122A VAL* 4.2 4.9 - - + +
174A THR* 3.6 31.9 - - + -
261A ARG 3.7 0.6 - - - +
262A ILE* 3.2 9.0 - - - +
263A ARG* 2.9 31.9 + - + +
265A PHE* 3.9 15.7 - - + -
278A VAL* 1.3 73.6 - - - +
280A ILE* 1.3 61.1 + - - +
281A CYS* 3.8 12.3 - - - -
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Residues in contact with ILE 280 (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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121A GLY 5.3 1.2 + - - -
123A LYS* 6.2 1.2 - - - +
127A SER* 4.0 21.1 - - - +
128A LEU* 3.9 18.4 - - + -
164A ARG* 3.6 31.0 - - + +
172A ASP* 3.9 37.1 - - + +
174A THR* 3.5 21.1 + - - -
260A ARG* 4.5 4.3 - - - -
261A ARG 3.6 2.2 - - - -
262A ILE* 4.1 20.6 - - + -
278A VAL* 3.8 16.2 - - + -
279A LEU* 1.3 81.6 - - - +
281A CYS* 1.3 62.3 + - - +
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Residues in contact with CYS 281 (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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114A LEU* 4.2 3.6 - - - -
172A ASP 3.7 7.0 - - - -
174A THR* 3.5 23.8 - - - +
176A ALA* 3.8 27.8 - - + +
260A ARG* 3.3 13.8 - - - +
261A ARG* 2.8 40.8 + - + +
279A LEU* 3.8 29.2 - - - -
280A ILE* 1.3 76.8 - - - +
282A ALA* 1.3 62.4 + - - +
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Residues in contact with ALA 282 (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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172A ASP 3.5 7.5 + - - -
174A THR 4.5 1.4 + - - -
179A ASN* 5.5 1.9 + - - +
187A ASP* 3.4 27.7 + - + +
189A PRO* 3.7 18.4 - - + -
241A PRO 4.8 2.9 - - - +
243A ARG* 3.5 35.7 - - - +
260A ARG* 4.4 1.1 - - - +
261A ARG* 3.4 15.2 - - - +
281A CYS* 1.3 77.7 - - - +
283A GLY* 1.3 59.3 + - - +
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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