Contacts of the helix formed by residues 322 - 328 (chain A) in PDB entry 1LT8
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 PRO 322 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A ARG 3.9 0.9 - - - +
66A ALA 3.4 34.3 - - - +
67A GLY* 3.6 9.4 - - - -
308A ARG* 4.2 7.9 - - + -
311A ALA* 3.4 25.4 - - + +
318A ARG* 5.5 0.9 - - - +
320A PHE* 4.3 9.8 - - + +
321A LEU* 1.3 93.5 - - + +
323A PRO* 1.3 76.2 - - + +
324A ALA 4.6 0.2 - - - +
325A SER* 3.1 37.1 + - - +
326A GLU* 4.4 1.9 + - - +
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Residues in contact with PRO 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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64A LEU 4.4 4.9 - - - +
65A ARG* 3.0 52.8 + - + +
67A GLY* 5.0 0.7 - - - +
320A PHE* 5.9 1.6 - - + -
321A LEU 4.0 1.1 - - - +
322A PRO* 1.3 84.0 - - + +
324A ALA* 1.3 58.5 + - - -
325A SER 3.1 0.2 - - - -
326A GLU* 3.2 40.2 + - - +
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Residues in contact with ALA 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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65A ARG* 2.8 44.6 + - + +
66A ALA* 3.8 12.3 - - + -
308A ARG* 3.0 38.6 + - + +
322A PRO 3.2 0.8 + - - -
323A PRO* 1.3 68.9 - - - +
325A SER* 1.3 55.4 + - - +
326A GLU 2.9 6.1 - - - -
327A LYS* 2.9 19.6 + - - +
36B ARG 5.5 0.4 - - - +
37B GLY* 4.4 10.3 - - - -
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Residues in contact with SER 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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308A ARG* 4.0 2.5 - - - +
312A GLU* 2.9 27.1 + - - +
321A LEU* 4.1 16.7 - - - +
322A PRO* 3.1 36.6 + - - +
324A ALA* 1.3 77.7 - - - +
326A GLU* 1.3 57.4 + - - +
327A LYS 3.0 2.2 - - - -
329A GLY* 2.4 44.7 + - - +
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Residues in contact with GLU 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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65A ARG* 4.9 8.1 + - - +
322A PRO 5.1 1.3 - - - +
323A PRO* 3.3 34.5 - - + +
324A ALA 2.9 0.8 - - - -
325A SER* 1.3 78.2 - - - +
327A LYS* 1.3 82.3 + - - +
328A HIS 3.5 0.9 - - - -
40B LYS* 4.7 6.4 - - - +
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Residues in contact with LYS 327 (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 ARG* 3.8 10.7 - - - +
308A ARG* 4.0 8.0 + - - +
324A ALA 2.9 9.6 + - - +
326A GLU* 1.3 110.7 + - - +
328A HIS* 1.3 58.4 + - - +
34B GLU* 4.6 2.9 - - - +
37B GLY 3.6 12.3 - - - +
38B TYR* 3.1 35.9 - - - +
39B VAL* 3.0 29.3 - - - +
40B LYS* 3.3 29.5 - - - -
41B ALA 4.1 2.6 + - - -
47B GLU* 3.2 24.8 + - + +
51B GLU* 4.7 10.4 + - - +
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Residues in contact with HIS 328 (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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278A ARG* 3.1 45.1 + - + -
279A TRP* 4.5 15.7 - + - -
282A GLN* 5.2 1.3 - - - -
308A ARG* 3.2 31.5 + - - +
312A GLU* 2.8 32.1 + - - +
324A ALA 4.3 0.4 - - - +
325A SER 3.3 0.6 + - - -
326A GLU 3.5 0.8 - - - -
327A LYS* 1.3 78.6 - - - +
329A GLY* 1.3 55.1 + - - +
330A SER* 2.6 40.7 + - - +
331A TRP* 5.4 1.6 - - - -
332A GLY 4.9 3.4 + - - -
334A GLY* 4.9 0.7 - - - -
34B GLU* 4.1 4.3 - - - -
40B LYS* 3.4 13.2 + - - +
41B ALA* 5.6 1.8 - - + +
269B PHE* 4.0 19.6 - + - -
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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