Contacts of the strand formed by residues 233 - 237 (chain A) in PDB entry 1T43
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 PHE 233 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A ARG* 3.1 49.6 - - + -
108A GLU* 4.8 6.7 - - - -
109A GLN* 5.0 6.5 - - - -
178A ALA 2.6 10.6 + - - -
179A MET* 3.3 9.9 - - + +
180A ILE* 2.8 34.2 + - - +
229A VAL* 5.3 4.5 - - - +
231A GLY 3.6 9.4 - - - -
232A GLY* 1.3 74.3 - - - -
234A LEU* 1.3 56.1 + - - +
235A LEU* 3.4 18.2 - - + -
257A ASP* 5.5 3.1 - - - -
259A GLU* 5.3 2.2 - - - -
272A LEU* 4.0 19.5 - - + -
273A GLY* 3.9 17.5 - - - -
274A ARG* 3.4 48.5 - - + -
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Residues in contact with LEU 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A ILE* 3.4 20.4 - - + +
220A ILE* 3.7 8.1 - - + -
221A ILE* 4.0 12.8 - - + -
224A SER* 3.5 23.3 - - - +
225A ARG* 4.5 12.6 - - + +
233A PHE* 1.3 74.1 - - - +
235A LEU* 1.3 67.4 + - - +
236A LEU* 3.5 33.4 - - + -
250A PHE* 3.4 41.3 - - + -
272A LEU* 3.3 22.3 - - - -
273A GLY 3.4 10.7 + - - +
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Residues in contact with LEU 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A LEU* 3.7 18.2 - - + +
101A GLN* 4.6 5.2 - - + +
102A ALA* 3.6 31.2 - - + +
105A ARG* 4.8 3.1 - - - -
179A MET* 3.6 28.3 - - + -
180A ILE 3.1 10.7 + - - +
181A VAL* 3.4 4.3 - - + -
182A SER 2.9 26.7 + - - -
233A PHE* 3.4 20.2 - - + -
234A LEU* 1.3 78.8 - - - +
236A LEU* 1.3 64.1 + - - +
270A VAL* 4.5 5.2 - - + -
271A THR 3.9 3.4 - - - -
272A LEU* 3.2 34.5 - - + -
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Residues in contact with LEU 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A LEU* 4.8 1.3 - - - -
182A SER* 3.2 20.6 - - - +
184A PRO* 4.3 10.8 - - + -
217A ILE* 4.2 21.3 - - + +
220A ILE* 3.0 44.9 - - + -
221A ILE* 3.9 19.7 - - + -
234A LEU* 3.5 9.9 - - + -
235A LEU* 1.3 84.9 - - - +
237A GLU* 1.3 62.6 + - - +
238A HIS* 3.5 6.9 - - + -
246A VAL* 5.3 0.9 - - + -
250A PHE* 4.3 6.7 - - + -
270A VAL* 3.0 29.6 - - - +
271A THR 3.0 18.2 + - - +
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Residues in contact with GLU 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A LEU* 5.8 0.7 - - - +
92A ARG* 5.5 4.0 - - - +
94A ASP* 5.0 1.7 - - - +
95A THR* 2.9 34.9 + - - +
98A LEU* 4.1 10.5 - - + +
182A SER 3.0 7.1 + - - -
183A ASN* 2.8 43.3 + - + +
184A PRO* 3.8 14.2 - - - +
186A TYR* 3.1 30.4 + - + +
217A ILE* 4.7 1.0 - - - +
236A LEU* 1.3 74.7 - - - +
238A HIS* 1.3 67.8 + - - +
269A ARG* 3.2 34.2 + - + +
270A VAL* 4.5 0.9 - - + +
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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
------------------------------------------------------------
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