Contacts of the strand formed by residues 296 - 301 (chain A) in PDB entry 4IX8
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 GLY 296 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A ILE* 3.6 8.3 - - - +
147A THR* 2.8 33.7 + - - +
149A GLY 3.6 10.2 - - - +
150A VAL* 4.2 1.6 - - - -
282A GLY 3.6 11.0 - - - -
283A GLY* 4.2 7.2 - - - -
295A VAL* 1.3 77.1 - - - +
297A TRP* 1.3 68.7 + - - +
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Residues in contact with TRP 297 (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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118A LEU* 5.5 1.3 - - + -
122A VAL* 3.7 29.9 - - + +
125A TYR* 4.0 24.2 - + - -
126A TRP* 3.6 23.5 - + - -
144A VAL* 4.5 4.9 - - + -
145A ILE 3.1 13.9 - - - +
146A ILE* 4.1 13.0 - - + -
147A THR* 3.3 10.0 + - - -
150A VAL* 4.9 0.8 - - - +
153A ALA* 4.2 5.2 - - - +
280A ILE* 4.8 1.3 - - - +
281A LEU* 3.5 3.8 - - - -
282A GLY* 2.9 40.1 + - - +
283A GLY* 3.5 38.8 - - - -
284A THR* 4.1 17.9 - - + -
287A TYR* 5.7 0.2 - + - -
295A VAL* 5.3 6.7 - - + -
296A GLY* 1.3 80.0 - - - +
298A SER* 1.3 62.3 + - - +
299A ILE* 3.9 19.5 - - + -
332A ILE* 5.0 6.5 - - + -
336A LEU* 4.2 18.8 - - + -
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Residues in contact with SER 298 (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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143A ASN 3.7 1.4 + - - +
144A VAL* 3.3 4.7 - - - +
145A ILE* 2.8 54.6 + - - +
147A THR* 4.6 3.0 - - - +
153A ALA* 4.4 9.4 - - - -
156A LEU* 6.1 0.2 - - - +
279A LEU* 4.0 17.1 - - - +
280A ILE 3.2 5.6 - - - -
281A LEU* 3.6 22.7 - - - -
297A TRP* 1.3 73.0 - - - +
299A ILE* 1.3 63.7 + - - +
300A LEU 4.3 0.2 - - - -
314A MET* 4.6 5.2 - - - +
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Residues in contact with ILE 299 (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* 4.0 16.6 - - + +
123A SER* 5.5 0.9 - - - -
126A TRP* 3.8 43.1 - - + -
139A LEU* 3.7 26.0 - - + -
140A LYS 5.2 3.4 - - - +
143A ASN* 3.4 7.0 - - + +
144A VAL* 4.1 17.9 - - + -
278A ARG 3.5 1.7 - - - +
279A LEU* 3.5 4.5 - - - -
280A ILE* 2.8 43.6 + - + +
297A TRP* 3.9 15.3 - - + +
298A SER* 1.3 79.8 - - - +
300A LEU* 1.3 68.2 + - - +
301A ILE* 3.8 4.9 + - + +
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Residues in contact with LEU 300 (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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138A ALA 4.8 1.7 - - - +
140A LYS 5.4 0.7 + - - -
143A ASN* 2.9 47.3 + - + +
277A PRO* 4.9 1.1 - - + -
278A ARG 3.5 20.6 - - - +
279A LEU* 3.9 12.9 - - + +
299A ILE* 1.3 73.7 - - - +
301A ILE* 1.3 65.1 + - - +
302A ASP* 4.0 24.9 - - + +
307A ALA* 4.1 16.2 - - + +
308A GLY* 5.5 0.4 - - - -
310A TRP* 4.2 25.6 - - + -
311A ALA* 3.8 31.4 - - + +
314A MET* 5.1 3.4 - - + -
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Residues in contact with ILE 301 (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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135A ARG 5.9 0.4 - - - +
138A ALA* 3.7 32.8 - - + +
139A LEU* 3.6 27.4 - - + -
143A ASN* 5.4 0.2 - - - +
269A VAL 5.3 0.2 - - - -
270A ALA* 3.6 38.4 - - + +
276A VAL 3.8 4.0 - - - +
277A PRO* 3.5 3.5 - - - +
278A ARG* 2.9 60.5 + - + +
280A ILE* 3.8 15.0 - - + -
299A ILE* 4.3 6.1 - - + +
300A LEU* 1.3 76.6 - - - +
302A ASP* 1.3 62.3 + - - +
303A PRO* 3.8 3.3 - - + +
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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