Contacts of the strand formed by residues 291 - 298 (chain A) in PDB entry 4CAA
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 291 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288A LEU* 5.4 2.9 - - + -
289A PRO* 3.0 30.7 - - + -
290A LYS* 1.3 77.3 - - - +
292A SER* 1.3 63.9 + - - +
293A ILE* 4.0 18.8 - - + -
338A LEU* 3.6 27.6 - - + -
339A ASP* 3.7 0.2 - - - -
340A VAL* 2.7 71.1 + - + +
341A PHE* 4.2 5.8 - - - -
370B PHE* 4.2 12.8 - + - -
372B MET* 4.4 9.4 - - - -
386B SER* 5.5 0.2 - - - -
388B VAL* 3.7 30.1 - - + -
391B PRO* 3.9 28.0 - - + +
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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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291A PHE* 1.3 77.3 - - - +
293A ILE* 1.3 65.8 + - - +
294A SER* 5.9 0.5 - - - -
337A VAL* 4.8 3.1 - - - +
338A LEU 3.3 7.8 + - - -
339A ASP* 2.6 28.7 + - - -
341A PHE* 4.2 12.1 - - - -
391B PRO 4.6 5.4 + - - +
393B GLN* 2.8 19.1 + - - -
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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* 3.8 28.9 - - + +
50A VAL 4.1 3.6 - - - +
51A ILE* 3.7 22.2 - - + +
291A PHE* 4.0 29.2 - - + -
292A SER* 1.3 81.7 - - - +
294A SER* 1.3 60.3 + - - +
295A ARG* 3.8 9.6 - - - +
337A VAL* 3.6 2.1 - - - +
338A LEU* 3.0 36.3 + - + +
386B SER* 3.6 23.8 - - - +
388B VAL* 4.1 11.0 - - + -
390B ASN 5.0 1.1 - - - +
391B PRO* 4.9 7.0 - - + +
393B GLN* 3.5 7.9 - - - +
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Residues in contact with SER 294 (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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51A ILE* 4.6 0.2 - - - -
292A SER* 5.9 0.7 - - - -
293A ILE* 1.3 75.0 - - - +
295A ARG* 1.3 78.2 + - - +
335A LYS* 2.9 26.9 + - - -
336A ALA 3.4 6.4 + - - -
337A VAL* 3.8 16.9 - - - +
393B GLN* 3.8 11.7 + - - +
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Residues in contact with ARG 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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48A LYS* 3.3 25.4 - - - +
49A ASN* 3.1 47.3 + - - +
51A ILE* 3.5 20.8 - - + +
293A ILE* 3.8 4.2 - - - +
294A SER* 1.3 94.5 + - - +
296A ASP* 1.3 61.3 + - - +
297A TYR* 3.3 31.1 - - + +
335A LYS* 3.8 2.0 - - - +
336A ALA* 3.0 30.9 + - - +
393B GLN* 2.8 49.9 + - - +
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Residues in contact with ASP 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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295A ARG* 1.3 74.9 - - - +
297A TYR* 1.3 74.4 + - - +
334A HIS 3.2 10.5 - - - +
335A LYS* 4.1 25.9 + - + +
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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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41A LEU* 3.6 35.2 - - + -
49A ASN 4.7 0.7 + - - -
50A VAL* 3.9 10.8 - - + +
51A ILE 3.4 34.0 + - - -
52A PHE* 4.2 9.9 - - + -
295A ARG* 3.3 33.2 - - + +
296A ASP* 1.3 82.6 - - - +
298A ASN* 1.3 61.6 + - - +
299A LEU* 3.9 19.3 - - + -
333A VAL* 3.3 8.1 - - - +
334A HIS* 2.7 51.1 + + - +
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Residues in contact with ASN 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 75.6 - - - +
299A LEU* 1.3 61.0 + - - +
300A ASN* 3.2 25.6 - - - +
301A ASP* 4.2 11.8 + - - +
302A ILE* 5.2 4.2 - - - +
331A GLN* 3.0 39.2 - - - +
332A VAL 3.7 3.8 - - - -
333A VAL* 4.4 4.7 - - + +
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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