Contacts of the strand formed by residues 260 - 269 (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 ARG 260 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164A ARG* 3.6 22.9 - - + +
165A HIS* 3.0 28.6 + - - +
168A GLY* 3.3 20.8 + - - -
169A SER 2.9 24.9 + - - -
172A ASP* 2.7 28.7 + - - +
189A PRO* 3.7 16.0 - - - +
190A ALA 3.0 24.2 + - - -
191A ILE 4.8 0.2 - - - -
192A GLY* 3.9 9.3 - - - +
258A GLN* 3.6 0.7 - - - +
259A GLY* 1.3 102.4 + - - +
261A ARG* 1.3 81.0 + - - +
262A ILE* 3.7 19.1 - - + -
280A ILE* 4.5 1.6 - - + -
281A CYS 3.3 17.3 - - - +
282A ALA* 4.4 1.1 - - - +
283A GLY* 3.5 3.4 - - - +
285A GLU* 5.3 4.0 + - - -
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Residues in contact with ARG 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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111A VAL* 3.6 14.8 - - + -
114A LEU* 3.5 23.8 - - + +
165A HIS* 4.9 0.2 - - - -
239A LEU* 3.6 30.1 - - - +
240A GLY 2.9 27.4 + - - +
241A PRO* 4.5 8.7 - - + +
242A THR 3.0 18.1 + - - -
243A ARG* 3.9 0.6 - - - +
258A GLN* 2.9 29.4 + - - +
260A ARG* 1.3 78.0 + - - +
262A ILE* 1.3 59.7 + - - +
280A ILE* 3.6 0.5 - - - -
281A CYS* 2.8 43.4 + - + -
282A ALA 3.4 18.4 - - - +
283A GLY* 3.6 8.2 - - - -
284A ASP* 2.9 30.1 + - - -
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Residues in contact with ILE 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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109A PHE 4.4 5.2 + - - +
110A GLN* 3.1 10.3 - - - +
111A VAL* 3.1 25.2 + - - +
114A LEU* 3.9 3.8 - - - +
128A LEU* 4.5 4.5 - - + -
161A LEU* 3.7 34.8 - - + -
164A ARG* 4.0 28.3 - - + -
165A HIS* 4.0 10.3 - - + +
260A ARG* 3.7 24.0 - - + -
261A ARG* 1.3 80.8 - - - +
263A ARG* 1.3 67.1 + - - +
264A LEU* 4.6 3.6 - - + +
278A VAL* 3.8 18.4 - - + -
279A LEU 3.2 10.1 - - - +
280A ILE* 4.1 11.9 - - + -
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Residues in contact with ARG 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A PRO* 6.3 0.7 - - + -
110A GLN* 4.0 6.1 - - + +
111A VAL 3.6 20.9 - - - +
112A ALA* 3.2 22.0 + - - +
113A ASP* 3.7 8.7 + - - +
114A LEU* 3.0 37.3 + - + +
115A GLU* 4.5 7.3 + - - +
262A ILE* 1.3 75.3 - - - +
264A LEU* 1.4 71.3 + - - +
265A PHE* 3.5 37.3 - - + -
278A VAL* 3.3 7.4 - - - +
279A LEU* 2.9 34.4 + - + -
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Residues in contact with LEU 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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101A LEU* 3.8 40.4 - - + -
102A PHE* 4.3 7.6 - - + -
110A GLN* 3.0 27.4 + - + +
128A LEU* 3.6 31.6 - - + -
157A ALA* 3.9 13.7 - - + +
161A LEU* 4.4 7.2 - - + -
262A ILE* 4.6 5.4 - - + -
263A ARG* 1.4 84.3 + - - +
265A PHE* 1.3 61.2 + - - +
266A PRO* 3.3 13.4 - - + +
275A VAL* 3.9 17.3 - - + -
277A ARG 4.0 2.9 - - - -
278A VAL* 3.9 11.7 - - + -
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Residues in contact with PHE 265 (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 4.4 4.7 - - - -
116A PRO* 6.0 1.3 - - + -
122A VAL* 4.0 25.8 - - + -
263A ARG* 3.5 66.4 - - + -
264A LEU* 1.3 71.0 - - - +
266A PRO* 1.3 65.9 - - - +
267A GLU* 4.9 0.2 - - - +
275A VAL* 4.5 2.0 - - - -
276A PRO* 3.3 21.0 - - - +
277A ARG* 3.0 62.5 + - + +
278A VAL* 3.9 0.4 - - - -
279A LEU* 3.9 19.7 - - + -
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Residues in contact with PRO 266 (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 3.7 32.8 - - + +
102A PHE* 3.6 49.4 - - + -
264A LEU 3.3 12.1 - - - +
265A PHE* 1.3 87.8 - - - +
267A GLU* 1.3 60.2 + - - +
273A ILE* 4.0 2.0 - - + -
274A VAL 3.3 13.0 - - - +
275A VAL* 4.4 3.1 - - + -
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Residues in contact with GLU 267 (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 3.9 7.9 - - - -
266A PRO* 1.3 75.2 - - - +
268A ARG* 1.3 73.3 + - - +
269A ARG* 3.1 40.9 + - + +
273A ILE* 3.6 0.3 - - - -
274A VAL* 2.8 34.4 + - - +
276A PRO* 3.7 18.4 - - + +
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Residues in contact with ARG 268 (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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2A GLU* 6.1 2.2 - - - +
3A PRO* 3.9 30.5 + - - +
4A GLU 3.6 22.2 + - - -
5A MSE 3.9 20.0 - - + +
267A GLU* 1.3 80.9 - - - +
269A ARG* 1.3 64.1 + - - +
270A GLY 3.5 19.1 + - - +
271A ASP* 3.8 19.6 + - - +
272A ALA 3.5 4.0 - - - +
273A ILE* 3.5 33.8 - - - +
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Residues in contact with ARG 269 (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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149A GLU 5.5 3.6 + - - -
151A ALA* 4.0 17.1 - - - +
267A GLU* 3.1 31.3 + - - +
268A ARG* 1.3 76.2 - - - +
270A GLY* 1.3 64.5 + - - +
271A ASP 3.3 0.3 + - - -
272A ALA* 2.8 31.6 + - + +
274A VAL* 3.6 25.2 - - + +
276A PRO* 3.6 20.6 - - - +
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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