Contacts of the helix formed by residues 314 - 323 (chain A) in PDB entry 4IKV
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 THR 314 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A ARG* 4.3 2.9 - - - +
47A VAL* 4.9 1.2 - - - +
67A LEU* 3.3 23.9 - - - +
70A MET* 3.8 21.1 - - + -
71A SER* 3.7 30.7 + - - +
310A GLU 4.2 4.3 - - - +
311A GLN* 3.1 25.4 + - - +
312A GLY 3.5 0.2 - - - -
313A SER* 1.3 92.6 - - - +
315A ILE* 1.3 77.0 + - - +
316A LEU 3.3 0.4 - - - -
317A ALA* 3.1 4.7 + - - +
318A ASN 2.9 18.9 + - - -
451A ASN* 5.2 1.9 + - - +
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Residues in contact with ILE 315 (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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67A LEU* 4.1 16.8 - - + -
311A GLN* 3.2 29.6 + - + +
314A THR* 1.3 87.2 + - - +
316A LEU* 1.3 58.8 + - + +
318A ASN* 3.1 6.8 + - - +
319A TYR* 2.8 25.3 + - - +
455A VAL* 4.7 16.4 - - + -
458A TYR* 3.6 58.0 + - + -
466A TYR* 3.6 9.6 - - + +
467A PHE* 3.9 21.8 - - + -
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Residues in contact with LEU 316 (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 ILE 5.9 1.1 - - - +
311A GLN 2.9 17.9 + - - +
312A GLY* 3.7 9.9 - - - +
315A ILE* 1.3 75.5 - - + +
317A ALA* 1.3 60.7 + - - +
319A TYR* 3.5 7.2 - - + +
320A ALA* 2.8 27.5 + - - +
382A PHE* 4.8 13.7 - - + -
385A ILE* 4.3 9.0 - - + -
402A LEU* 4.0 25.6 - - + +
405A SER* 3.9 21.1 - - - +
406A TYR* 3.4 32.4 + - + +
409A VAL* 5.9 4.5 - - + -
467A PHE* 4.0 32.3 - - + -
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Residues in contact with ALA 317 (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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44A ALA 6.0 0.4 - - - +
47A VAL* 4.0 14.8 - - + -
48A TYR* 2.7 34.8 + - + +
312A GLY 3.7 5.1 + - - -
313A SER 3.6 20.9 - - - +
314A THR 3.1 9.3 + - - +
316A LEU* 1.3 76.2 - - - +
318A ASN* 1.3 62.9 + - - +
320A ALA* 3.4 4.2 + - - -
321A ASP 3.2 12.0 + - - -
335A PRO 5.5 0.2 - - - -
339A GLN* 3.9 18.4 - - + +
406A TYR* 4.6 0.2 - - - -
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Residues in contact with ASN 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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47A VAL* 5.4 0.8 - - + +
48A TYR* 4.7 0.4 - - - -
51A TYR* 3.2 33.0 + - + +
63A GLU* 2.9 30.5 + - - +
67A LEU* 4.0 23.2 - - + +
314A THR 2.9 12.4 + - - +
315A ILE* 3.3 8.5 - - - +
317A ALA* 1.3 73.1 - - - +
319A TYR* 1.3 60.7 + - - +
321A ASP* 3.1 2.1 + - - -
322A LYS* 2.9 37.2 + - - +
323A ARG* 5.6 0.5 - - - +
458A TYR* 3.4 21.9 + - + -
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Residues in contact with TYR 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 ILE 2.8 13.8 + - - +
316A LEU* 3.5 18.6 - - + +
317A ALA 3.3 0.2 - - - -
318A ASN* 1.3 77.6 + - - +
320A ALA* 1.3 62.3 - - - +
323A ARG* 2.9 45.5 + - + -
324A THR* 3.1 25.9 + - - -
385A ILE* 3.7 37.7 + - + +
388A PRO* 4.0 2.1 - - - +
389A GLY 4.6 2.6 + - - -
397A VAL* 3.1 33.4 - - + +
402A LEU* 3.9 16.8 - - + -
458A TYR* 3.6 20.4 - - - +
463A GLU* 4.0 20.7 + - - -
467A PHE* 4.1 12.8 - + + -
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Residues in contact with ALA 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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48A TYR* 4.1 0.4 - - - +
316A LEU 2.8 14.6 + - - +
317A ALA* 3.5 11.2 - - - +
319A TYR* 1.3 76.8 - - - +
321A ASP* 1.3 60.0 + - - +
324A THR* 3.4 26.3 + - - -
326A LEU* 3.4 17.2 - - - +
335A PRO* 3.9 14.8 - - + +
338A PHE* 3.8 24.5 - - + -
402A LEU* 3.7 14.6 - - + -
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Residues in contact with ASP 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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48A TYR* 3.3 20.2 - - + -
51A TYR* 2.5 41.8 + - - +
52A TYR* 2.6 32.6 + - - -
317A ALA 3.2 2.2 + - - +
318A ASN 3.1 1.6 + - - +
320A ALA* 1.3 81.7 - - - +
322A LYS* 1.3 69.0 + - - +
324A THR 5.0 1.5 - - - +
326A LEU* 4.4 10.7 - - - +
335A PRO* 3.8 12.8 - - + +
396A LEU* 5.8 0.3 - - - +
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Residues in contact with LYS 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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51A TYR* 4.4 6.3 - - + -
63A GLU* 3.6 29.7 + - - +
318A ASN* 2.9 26.2 + - - +
321A ASP* 1.3 97.5 - - - +
323A ARG* 1.3 73.0 + - + +
324A THR 3.8 1.1 - - - -
396A LEU* 3.5 14.1 - - - +
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Residues in contact with ARG 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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318A ASN* 5.6 0.9 - - - +
319A TYR* 2.9 43.1 + - + +
322A LYS* 1.3 90.9 + - + +
324A THR* 1.3 59.2 + - - +
389A GLY* 3.6 22.6 + - - -
392A SER* 5.1 0.8 + - - -
394A GLY* 5.2 3.8 - - - -
395A GLY 3.1 31.1 + - - +
396A LEU* 3.4 10.7 - - - +
397A VAL* 2.9 32.4 + - - +
458A TYR* 4.4 4.5 - - - +
460A PRO* 5.7 11.5 - - - +
463A GLU* 2.7 38.8 + - - +
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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