Contacts of the strand formed by residues 361 - 368 (chain A) in PDB entry 5INQ
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 361 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A ILE* 5.0 0.2 - - - -
128A THR 3.4 11.2 - - - -
129A TRP* 3.4 22.7 - - - +
344A LEU* 3.3 10.6 - - - +
345A VAL* 2.9 42.4 + - - -
360A TRP* 1.3 75.4 - - - +
362A LEU* 1.3 61.5 + - - -
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Residues in contact with LEU 362 (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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126A PHE* 3.7 1.9 - - - +
127A ILE* 3.1 8.4 - - - +
128A THR* 3.0 45.9 + - + +
303A CYS* 4.2 7.4 - - + +
306A THR* 4.0 12.6 - - + -
326A ASP* 3.5 39.0 - - + +
327A ARG* 4.5 1.6 - - - +
328A ILE* 4.2 15.5 - - + -
342A LEU* 4.0 30.3 - - + -
343A ASP 3.5 4.7 - - - +
344A LEU* 3.7 25.6 - - + -
345A VAL* 4.2 0.4 - - - +
360A TRP 4.2 0.2 + - - -
361A GLY* 1.3 74.3 - - - -
363A LEU* 1.3 60.1 + - - +
364A CYS* 4.0 0.7 + - - +
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Residues in contact with LEU 363 (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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125A SER* 5.1 6.1 - - - -
126A PHE 3.4 18.2 - - - +
127A ILE* 3.7 18.6 - - + -
153A TYR* 3.7 46.7 - - + -
155A PRO* 4.9 4.5 - - + -
341A SER* 4.0 1.9 + - - +
342A LEU* 3.4 5.5 + - - +
343A ASP* 2.8 52.7 + - + +
345A VAL* 4.0 15.6 - - + +
361A GLY 4.2 0.2 - - - -
362A LEU* 1.3 71.7 - - - +
364A CYS* 1.3 64.8 + - - +
365A THR* 5.3 6.1 - - + -
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Residues in contact with CYS 364 (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 ILE 4.0 0.5 - - - +
125A SER* 3.3 3.3 - - - -
126A PHE* 2.8 61.4 + - + -
293A ALA* 4.6 7.6 - - - -
297A LEU* 5.8 0.2 - - - -
328A ILE* 3.8 11.7 - - + -
339A PRO* 5.2 1.1 - - - -
341A SER* 3.4 11.7 - - - -
342A LEU* 3.7 14.8 - - + -
362A LEU 4.0 0.4 + - - +
363A LEU* 1.3 76.1 - - - +
365A THR* 1.3 64.0 + - - +
366A LEU* 3.3 33.0 - - - -
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Residues in contact with THR 365 (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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123A THR* 5.4 7.9 - - - +
124A ILE 3.4 5.8 - - - -
125A SER* 3.8 18.2 - - - -
340A GLN* 2.7 43.1 + - - +
341A SER* 2.6 33.2 + - - +
363A LEU* 5.3 9.6 - - + -
364A CYS* 1.3 78.8 - - - +
366A LEU* 1.3 61.9 + - - +
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Residues in contact with LEU 366 (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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123A THR* 3.2 4.4 - - - -
124A ILE* 2.9 38.9 + - + +
126A PHE* 4.0 14.4 - - + -
268A ILE* 3.6 33.2 - - + -
293A ALA* 5.0 3.1 - - + -
328A ILE* 5.6 1.8 - - + -
330A PHE* 5.2 4.5 - - + -
337A LEU* 3.9 28.5 - - + -
338A ILE 3.5 5.8 - - - +
339A PRO* 3.3 32.8 - - + -
340A GLN* 4.1 0.7 - - - +
364A CYS* 3.3 29.8 - - - -
365A THR* 1.3 72.5 - - - +
367A ASN* 1.3 66.0 + - - +
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Residues in contact with ASN 367 (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 SER* 3.6 11.6 + - - +
123A THR* 3.1 30.4 - - - +
336A HIS 3.7 0.2 - - - +
337A LEU* 3.4 7.7 - - - +
338A ILE* 2.9 33.3 + - + +
340A GLN* 3.2 39.6 + - - +
366A LEU* 1.3 74.0 - - - +
368A VAL* 1.3 63.0 + - - +
369A VAL* 3.9 16.4 + - + +
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Residues in contact with VAL 368 (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 SER* 2.9 33.7 + - - +
124A ILE* 4.8 8.7 - - + +
228A ASN* 3.6 39.2 + - + +
230A PHE* 3.7 28.3 - - + -
266A THR* 4.8 12.3 - - - +
336A HIS* 3.4 11.0 - - + +
337A LEU* 4.3 8.7 - - + -
367A ASN* 1.3 75.3 - - - +
369A VAL* 1.3 65.3 + - - +
370A LEU 4.3 0.3 + - - -
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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