Contacts of the strand formed by residues 323 - 331 (chain A) in PDB entry 4FMF
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 323 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246A GLU* 3.5 20.0 - - - -
247A PRO* 3.9 7.4 - - - -
319A THR* 3.4 3.1 + - - +
320A ASN* 2.4 38.5 + - - +
322A ILE* 1.3 78.1 - - - +
324A THR* 1.3 70.1 + - - -
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Residues in contact with THR 324 (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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246A GLU* 4.0 6.8 - - - +
247A PRO* 4.1 2.1 - - - +
317A GLU* 4.1 22.0 - - + +
318A ALA 3.2 12.3 - - - +
319A THR* 2.4 28.5 + - - +
323A GLY* 1.3 75.7 + - - -
325A ARG* 1.3 80.9 + - - +
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Residues in contact with ARG 325 (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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161A LYS* 3.2 31.6 - - - +
246A GLU* 4.1 15.3 + - + +
247A PRO* 3.3 29.7 - - + +
248A GLU* 5.5 0.2 - - - -
249A VAL* 3.5 8.7 - - + +
317A GLU* 3.5 3.2 - - - -
318A ALA 3.0 30.8 + - - +
324A THR* 1.3 85.9 - - - +
326A SER* 1.3 71.4 + - - +
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Residues in contact with SER 326 (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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249A VAL* 3.7 12.7 + - - +
315A ILE* 5.0 8.1 - - - +
316A CYS 3.1 15.9 - - - -
317A GLU* 3.7 18.6 - - - -
325A ARG* 1.3 89.5 + - - +
327A GLY* 1.3 63.5 + - - +
328A GLN* 5.7 3.2 + - - +
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Residues in contact with GLY 327 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249A VAL* 3.6 24.6 - - - +
250A THR* 5.7 0.2 - - - -
251A ILE* 3.6 8.1 - - - -
315A ILE* 3.1 26.2 - - - +
316A CYS 3.2 7.6 + - - -
326A SER* 1.3 74.9 - - - +
328A GLN* 1.3 67.4 + - - +
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Residues in contact with GLN 328 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251A ILE* 3.5 9.5 + - - +
285A LEU* 5.2 10.6 - - - +
313A THR* 3.8 18.7 - - + +
314A TYR 3.1 8.5 - - - +
315A ILE* 3.6 19.9 - - + +
326A SER* 5.8 3.6 + - - +
327A GLY* 1.3 80.3 - - - +
329A VAL* 1.3 73.9 + - - +
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Residues in contact with VAL 329 (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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251A ILE* 3.6 39.7 - - + +
254A PHE* 4.0 24.2 - - + -
267A LEU* 4.8 7.9 - - + -
312A GLY 3.4 3.8 - - - +
313A THR* 3.2 8.6 - - - -
314A TYR* 2.9 31.8 + - + +
328A GLN* 1.3 87.4 - - - +
330A GLU* 1.3 66.6 + - - +
331A VAL* 3.6 23.9 - - + +
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Residues in contact with GLU 330 (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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254A PHE* 3.8 15.6 - - - -
312A GLY* 4.3 3.8 - - - +
313A THR* 4.7 11.7 + - - +
329A VAL* 1.3 75.7 - - - +
331A VAL* 1.3 65.7 + - - +
332A ASN* 3.9 7.7 + - - +
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Residues in contact with VAL 331 (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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254A PHE* 3.6 7.9 - - + -
258A TRP* 3.5 35.0 - - + -
267A LEU* 4.6 3.6 - - + -
302A PHE* 5.9 0.2 - - + -
310A LEU* 3.7 20.4 - - + +
311A ALA* 3.9 9.9 - - - +
312A GLY 3.5 25.4 + - - +
314A TYR* 3.5 28.7 - - + -
329A VAL* 3.6 22.2 - - + +
330A GLU* 1.3 74.9 - - - +
332A ASN* 1.3 70.7 + - - +
333A ILE* 4.3 2.4 + - + -
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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