Contacts of the helix formed by residues 318 - 333 (chain A) in PDB entry 3LC4
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 TYR 318 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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314A ILE* 3.3 15.2 + - + +
315A LEU* 3.5 8.5 + - - +
316A MET 3.3 0.6 - - - -
317A LYS* 1.3 113.7 + - + +
319A PRO* 1.3 67.5 - - - +
320A GLU* 3.1 3.8 - - + -
321A ILE* 2.9 38.8 + - + +
322A GLU 3.5 3.6 + - - -
360A PHE* 5.7 0.5 - - - -
408A LYS* 4.8 13.7 + - - +
409A PHE* 3.6 54.5 + + + +
471A LEU* 4.2 11.2 - - + +
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Residues in contact with PRO 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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315A LEU 3.9 8.3 - - - +
316A MET* 4.0 4.9 - - - +
317A LYS 3.2 11.4 - - - +
318A TYR* 1.3 83.4 - - - +
320A GLU* 1.3 65.7 + - + +
322A GLU* 3.2 10.3 + - + +
323A GLU* 3.0 38.3 + - - +
466A PRO* 4.0 27.1 - - + -
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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
----------------------------------------------------------
318A TYR* 3.0 1.5 + - + -
319A PRO* 1.3 86.4 - - + +
321A ILE* 1.3 59.6 + - + +
323A GLU* 3.9 7.8 - - - +
324A LYS* 3.2 33.3 + - - +
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Residues in contact with ILE 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A LEU* 4.2 12.8 - - + -
318A TYR* 2.9 36.0 + - + +
320A GLU* 1.3 78.3 - - + +
322A GLU* 1.3 65.1 + - - +
324A LYS* 3.3 2.4 + - - +
325A LEU* 2.9 23.2 + - + +
349A TYR* 3.5 32.3 - - + +
353A VAL* 3.8 22.2 - - + -
409A PHE* 4.1 13.2 - - + +
411A PRO* 3.9 25.8 - - + -
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Residues in contact with GLU 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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315A LEU* 4.1 24.0 + - + +
316A MET* 5.5 1.2 - - - -
318A TYR 3.5 2.6 + - - -
319A PRO* 3.2 12.9 + - - +
321A ILE* 1.3 78.4 - - - +
323A GLU* 1.3 57.0 + - - +
325A LEU* 3.0 11.9 + - - +
326A HIS* 2.8 65.4 + - - +
455A LEU* 4.2 14.4 - - + +
459A ASN* 3.5 7.7 + - - -
460A LEU* 2.9 54.7 + - + +
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Residues in contact with GLU 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 PRO* 3.0 30.3 + - - +
320A GLU* 3.9 8.5 - - - +
321A ILE 3.3 0.2 - - - -
322A GLU* 1.3 81.6 - - - +
324A LYS* 1.3 63.6 + - + +
326A HIS* 3.4 9.3 + - - +
327A GLU* 3.0 23.6 + - - +
459A ASN* 3.8 20.6 + - - -
492A ARG* 5.7 0.7 + - - -
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Residues in contact with LYS 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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320A GLU* 3.2 20.0 + - - +
321A ILE 3.6 0.2 - - - +
323A GLU* 1.3 77.7 - - - +
325A LEU* 1.3 61.9 + - - +
327A GLU* 3.5 14.3 + - - +
328A GLU* 3.4 18.5 + - - +
349A TYR* 3.2 48.0 + - + +
412A GLU* 6.0 0.4 + - - -
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Residues in contact with LEU 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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315A LEU* 4.6 13.5 - - + -
321A ILE 2.9 11.5 + - - +
322A GLU* 3.2 10.1 - - - +
324A LYS* 1.3 74.1 - - - +
326A HIS* 1.3 66.2 + - - +
328A GLU* 3.1 7.7 + - - +
329A ILE* 3.0 27.6 + - + +
349A TYR* 3.6 17.5 - - + -
350A MET* 3.4 52.8 - - + +
353A VAL* 3.8 28.0 - - + -
455A LEU* 3.6 28.7 - - + -
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Residues in contact with HIS 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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322A GLU* 2.8 57.3 + - + +
323A GLU* 3.5 15.9 - - + +
325A LEU* 1.3 73.8 - - - +
327A GLU* 1.3 63.6 + - - +
328A GLU 3.1 0.5 + - - -
329A ILE* 3.1 9.3 + - - +
330A ASP* 3.0 28.5 + - - +
455A LEU* 3.0 40.0 + - + +
458A PHE 3.1 15.5 - - - -
459A ASN* 3.2 16.4 + - - -
492A ARG* 3.2 30.6 + - - +
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Residues in contact with GLU 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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323A GLU 3.0 10.8 + - - +
324A LYS* 3.5 15.9 - - - +
326A HIS* 1.3 78.3 - - - +
328A GLU* 1.3 56.6 + - - +
330A ASP* 3.5 6.1 + - - +
331A ARG* 2.6 81.9 + - - +
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Residues in contact with GLU 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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324A LYS 3.4 7.4 + - - +
325A LEU* 3.1 10.2 + - - +
326A HIS 3.1 0.6 - - - -
327A GLU* 1.3 76.5 + - - +
329A ILE* 1.3 57.2 + - + +
331A ARG* 3.6 30.6 + - - +
332A VAL* 2.7 48.7 + - + +
347A MET* 3.3 23.0 - - + +
348A PRO* 2.9 26.0 - - - +
349A TYR* 3.2 15.6 + - - +
350A MET* 2.9 30.1 + - + +
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Residues in contact with ILE 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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325A LEU 3.0 21.4 + - - +
326A HIS* 3.5 9.2 - - - +
328A GLU* 1.3 74.3 - - - +
330A ASP* 1.3 65.1 + - - +
333A ILE* 2.7 38.7 + - + +
334A GLY 3.1 10.2 + - - +
339A PRO* 6.2 0.2 - - + -
347A MET* 4.7 10.3 - - - -
350A MET* 5.1 6.7 - - + -
452A CYS* 3.7 29.2 - - - +
455A LEU* 3.5 37.2 - - + -
456A GLN* 3.7 35.0 - - + +
492A ARG* 5.5 0.2 - - - +
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Residues in contact with ASP 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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326A HIS 3.0 15.5 + - - +
327A GLU* 3.7 6.0 - - - +
329A ILE* 1.3 83.1 - - - +
331A ARG* 1.3 66.4 + - - +
334A GLY* 3.3 23.0 + - - +
335A PRO* 4.7 21.2 - - + +
456A GLN 4.9 1.2 - - - +
492A ARG* 3.0 31.5 + - - -
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Residues in contact with ARG 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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327A GLU* 2.6 71.6 + - - +
328A GLU* 3.6 38.9 + - - +
330A ASP* 1.3 75.3 - - - +
332A VAL* 1.3 69.7 + - + +
334A GLY 5.1 0.2 + - - -
346A GLU 4.9 4.6 + - - -
348A PRO* 5.0 3.0 - - - +
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Residues in contact with VAL 332 (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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328A GLU* 2.7 31.6 + - + +
331A ARG* 1.3 91.1 - - + +
333A ILE* 1.3 62.3 + - + +
337A ARG* 3.8 9.2 + - - -
343A ASP* 4.7 7.4 - - + +
346A GLU* 3.8 42.2 - - + +
347A MET* 3.9 20.4 - - + -
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Residues in contact with ILE 333 (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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329A ILE* 2.7 23.6 + - + +
332A VAL* 1.3 78.4 - - - +
334A GLY* 1.3 60.4 + - - +
337A ARG* 3.1 69.6 + - - +
339A PRO* 4.2 26.9 - - + -
343A ASP* 4.1 7.4 - - - +
347A MET* 3.4 36.6 - - + -
452A CYS* 4.4 4.7 - - - -
456A GLN* 3.4 11.7 - - - +
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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