Contacts of the strand formed by residues 291 - 298 (chain A) in PDB entry 3CWL
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 LEU 291 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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289A PRO* 3.5 35.2 + - + +
290A LYS* 1.3 75.9 - - - +
292A SER* 1.3 61.9 + - - +
293A ILE* 4.2 29.4 - - + -
338A LEU* 4.5 3.6 - - + -
339A THR* 3.4 4.0 - - - +
340A ILE* 2.7 64.2 + - + +
370A PHE* 4.4 4.9 - - + -
372A PHE* 6.2 0.4 - - + -
388A VAL* 4.1 25.8 - - + -
391A PRO* 4.3 20.4 - - + +
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Residues in contact with SER 292 (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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189A PHE* 5.8 0.2 - - - -
291A LEU* 1.3 76.8 - - - +
293A ILE* 1.3 67.7 + - - +
294A THR* 5.4 2.3 - - - +
337A VAL* 4.6 9.7 - - - +
338A LEU 3.1 12.3 + - - -
339A THR* 3.6 15.7 + - - -
391A PRO 4.6 1.9 + - - +
394A LYS* 3.3 38.9 - - - +
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Residues in contact with ILE 293 (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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49A ASN* 3.3 32.5 - - + +
50A ILE 4.4 4.9 - - - +
51A PHE* 3.6 27.6 - - + -
291A LEU* 4.2 18.2 - - + -
292A SER* 1.3 79.9 - - - +
294A THR* 1.3 68.3 + - - +
336A ALA 3.9 0.2 - - - +
337A VAL* 3.5 0.3 - - - +
338A LEU* 2.8 50.2 + - + +
372A PHE* 3.7 28.9 - - + -
387A LYS 4.9 1.8 - - - +
388A VAL* 4.5 11.2 - - + -
391A PRO* 5.2 4.7 - - + +
393A GLN 5.0 3.1 - - - +
394A LYS* 6.0 1.6 - - - -
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Residues in contact with THR 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ASN* 5.2 9.0 - - - +
51A PHE* 4.5 6.9 + - - +
292A SER* 5.4 2.7 - - - +
293A ILE* 1.3 84.9 - - - +
295A GLY* 1.3 58.3 + - - +
296A THR* 4.1 3.7 + - - -
335A LYS* 4.1 20.6 + - - +
336A ALA 3.0 9.2 - - - -
337A VAL* 3.7 27.4 - - + -
393A GLN* 5.9 0.7 + - - -
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Residues in contact with GLY 295 (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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49A ASN 5.8 1.3 - - - -
51A PHE* 3.3 23.1 + - - +
294A THR* 1.3 74.9 - - - +
296A THR* 1.3 62.2 + - - -
297A TYR* 3.5 18.5 - - - -
334A HIS 3.7 1.4 - - - +
335A LYS* 3.4 4.7 - - - +
336A ALA* 2.9 32.7 + - - +
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Residues in contact with THR 296 (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 LEU* 4.5 14.8 - - + +
294A THR* 4.1 4.3 + - - -
295A GLY* 1.3 70.7 - - - -
297A TYR* 1.3 73.8 + - - +
333A VAL* 4.6 7.9 - - + -
334A HIS 3.5 5.8 - - - +
335A LYS* 3.3 35.9 + - + +
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Residues in contact with TYR 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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37A LEU* 6.4 0.2 - - + -
41A LEU* 3.6 38.4 - - + -
44A GLN* 6.0 0.4 - - - -
49A ASN 4.3 3.1 + - - -
50A ILE* 3.6 14.8 - - + +
51A PHE 3.1 45.1 + - - -
52A PHE* 3.8 9.6 - - + -
57A ILE* 5.7 1.1 - - + -
295A GLY* 3.5 18.8 - - - -
296A THR* 1.3 81.4 - - - +
298A ASP* 1.3 61.5 + - - +
299A LEU* 3.4 12.3 + - + -
302A VAL* 4.6 9.4 - - + -
333A VAL* 3.5 8.6 - - - +
334A HIS* 2.8 59.3 + + + +
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Residues in contact with ASP 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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297A TYR* 1.3 69.2 - - - +
299A LEU* 1.3 57.3 + - - +
300A LYS* 2.9 25.9 + - - +
301A SER* 3.0 22.2 + - - -
302A VAL* 2.8 33.7 + - + +
332A ALA 3.8 7.7 + - - +
333A VAL* 5.0 3.8 - - + +
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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