Contacts of the helix formed by residues 317 - 325 (chain A) in PDB entry 4K8T
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 SER 317 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A ASN* 3.6 7.6 + - - -
305A ILE* 5.5 0.2 - - - +
316A THR* 1.3 74.4 + - - +
318A LEU* 1.3 59.5 + - - +
319A SER* 3.3 9.9 + - - -
320A GLU* 3.1 38.3 + - - +
321A ALA* 3.1 24.3 + - - +
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Residues in contact with LEU 318 (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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65A GLY* 3.6 23.8 - - - +
68A ASN* 2.9 29.6 + - + +
69A LEU* 3.8 23.4 - - + +
277A LEU* 4.0 22.0 - - + -
301A LEU* 4.9 1.5 - - + +
302A ALA* 4.3 14.8 - - + -
305A ILE* 3.7 29.1 - - + +
314A PRO* 4.0 22.4 - - + -
316A THR 3.2 0.9 + - - +
317A SER* 1.3 70.5 - - - +
319A SER* 1.3 61.0 + - - +
321A ALA* 3.1 5.5 + - - +
322A ALA* 2.8 30.3 + - - +
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Residues in contact with SER 319 (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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68A ASN 3.7 12.1 + - - -
69A LEU* 3.3 28.0 - - - +
70A GLY* 4.6 1.3 - - - -
317A SER* 3.3 9.9 + - - -
318A LEU* 1.3 78.9 - - - +
320A GLU* 1.3 63.3 + - - +
322A ALA* 3.3 7.5 + - - +
323A LYS* 2.9 42.4 + - - +
328A ILE 4.3 2.5 - - - +
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Residues in contact with GLU 320 (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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317A SER* 3.1 28.1 + - - +
319A SER* 1.3 82.2 + - - +
321A ALA* 1.3 59.6 + - - +
323A LYS* 3.2 22.3 + - - +
324A GLN* 2.9 30.9 + - - +
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Residues in contact with ALA 321 (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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301A LEU* 3.9 7.8 - - + +
305A ILE* 3.5 31.2 - - + -
317A SER 3.1 14.1 + - - +
318A LEU 3.1 8.7 + - - +
320A GLU* 1.3 76.3 - - - +
322A ALA* 1.3 51.2 + - - +
324A GLN* 3.4 13.4 + - - +
325A ALA* 2.8 35.0 + - - +
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Residues in contact with ALA 322 (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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69A LEU* 4.3 10.1 - - + -
284A TYR* 5.8 0.9 - - + -
298A LEU* 4.0 26.2 - - + -
301A LEU* 3.6 13.6 - - + +
318A LEU 2.8 18.4 + - - +
319A SER* 3.6 5.2 - - - +
321A ALA* 1.3 70.9 - - - +
323A LYS* 1.3 63.5 + - - +
325A ALA* 3.4 1.7 + - - -
326A GLY 3.3 2.4 + - - -
327A LEU* 3.0 13.8 + - - +
328A ILE 2.9 30.9 + - - +
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Residues in contact with LYS 323 (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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319A SER* 2.9 27.0 + - - +
320A GLU* 3.2 26.2 + - - +
322A ALA* 1.3 76.2 - - - +
324A GLN* 1.3 62.6 + - - +
326A GLY* 3.4 11.8 + - - -
328A ILE* 3.7 30.3 + - + +
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Residues in contact with GLN 324 (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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320A GLU 2.9 17.1 + - - +
321A ALA* 3.6 11.8 - - - +
323A LYS* 1.3 76.1 - - - +
325A ALA* 1.3 60.8 + - - +
326A GLY* 3.2 1.3 + - - -
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Residues in contact with ALA 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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301A LEU* 3.9 25.8 - - + -
321A ALA 2.8 18.9 + - - +
322A ALA 3.7 6.5 - - - +
323A LYS 3.2 0.8 - - - -
324A GLN* 1.3 75.4 - - - +
326A GLY* 1.3 60.1 + - - +
327A LEU* 3.6 16.9 + - + +
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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
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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