Contacts of the helix formed by residues 338 - 349 (chain A) in PDB entry 4KPD
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 338 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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329A ILE* 4.1 16.3 - - + +
333A ALA* 4.2 18.2 - - + -
336A LEU 3.2 7.1 - - - +
337A PRO* 1.4 82.2 - - + +
339A ALA* 1.4 55.8 + - - +
341A PHE* 3.0 10.8 + - + +
342A LEU* 2.9 37.0 + - + +
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Residues in contact with ALA 339 (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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66A VAL* 6.0 0.3 - - - +
70A GLU* 4.0 22.2 - - + +
337A PRO* 3.0 9.0 + - + +
338A PRO* 1.4 75.4 - - - +
340A VAL* 1.4 56.2 + - - +
342A LEU* 3.8 11.9 - - - +
343A GLY* 2.9 29.3 + - - -
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Residues in contact with VAL 340 (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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10A TYR* 4.9 2.6 + - - -
67A ALA* 4.5 7.6 - - + +
70A GLU* 3.3 28.9 - - + +
71A LEU* 4.4 14.4 - - + -
210A ILE* 3.7 44.0 - - + +
336A LEU* 5.1 5.4 - - + -
337A PRO* 3.0 36.8 + - + +
339A ALA* 1.4 78.7 - - - +
341A PHE* 1.3 71.9 + - + +
343A GLY* 4.8 0.2 - - - -
344A LEU* 4.1 11.8 + - - +
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Residues in contact with PHE 341 (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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210A ILE* 4.5 5.6 - - + -
228A ALA* 3.9 22.9 - - + -
231A ILE* 3.7 32.8 - - + -
232A LEU* 3.9 33.7 - - + -
235A MET* 4.0 6.3 - - - +
329A ILE* 3.7 22.4 - - + -
332A TYR 5.3 0.4 - - - -
333A ALA* 3.9 40.2 - - + -
336A LEU* 4.1 21.8 - - + -
337A PRO 4.4 1.6 - - - -
338A PRO 3.0 7.8 + - - +
340A VAL* 1.3 86.3 - - + +
342A LEU* 1.3 60.5 + - - +
343A GLY 3.4 0.6 + - - -
344A LEU* 3.5 5.1 + - - +
345A ALA* 3.0 28.1 + - - +
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Residues in contact with LEU 342 (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 TYR* 6.0 0.2 - - - +
326A MET* 3.7 32.0 - - + +
329A ILE* 3.8 21.5 - - + -
338A PRO* 2.9 22.0 + - + +
339A ALA* 4.0 8.5 - - - +
341A PHE* 1.3 75.4 - - - +
343A GLY* 1.3 58.9 + - - +
345A ALA* 3.7 4.7 - - - +
346A ARG* 2.9 32.6 + - - +
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Residues in contact with GLY 343 (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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9A VAL* 5.2 8.3 - - - -
10A TYR* 3.5 18.8 - - - -
66A VAL* 6.4 0.4 - - - -
339A ALA 2.9 18.8 + - - -
340A VAL 4.8 0.4 - - - -
341A PHE 3.4 0.2 - - - -
342A LEU* 1.3 75.2 - - - +
344A LEU* 1.3 56.5 + - - +
346A ARG* 3.5 4.0 + - - +
347A LYS* 3.1 27.2 + - - +
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Residues in contact with LEU 344 (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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10A TYR* 3.4 19.7 + - + +
59A ASN* 4.8 11.9 - - + -
63A THR* 3.6 36.8 - - + +
205A SER 5.1 2.9 - - - +
206A PHE* 3.7 36.6 - - + +
210A ILE* 4.6 3.4 - - + -
232A LEU* 4.4 13.2 - - + -
235A MET* 3.6 14.1 - - + -
340A VAL 4.1 7.8 + - - +
341A PHE* 3.5 8.5 + - - +
342A LEU 3.4 0.2 - - - -
343A GLY* 1.3 72.9 - - - +
345A ALA* 1.4 63.8 + - - +
347A LYS* 3.1 7.3 + - + +
348A ILE* 3.1 29.7 + - + +
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Residues in contact with ALA 345 (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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235A MET* 3.5 19.2 - - + +
322A TYR* 4.1 8.1 - - + -
325A ILE* 4.7 5.2 - - + -
326A MET* 3.8 26.0 - - + -
329A ILE* 4.7 2.5 - - + -
341A PHE 3.0 18.8 + - - +
342A LEU* 3.7 5.6 - - - +
344A LEU* 1.4 74.6 - - - +
346A ARG* 1.4 57.3 + - - +
348A ILE* 3.3 8.5 + - - +
349A TYR* 2.9 29.6 + - - +
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Residues in contact with ARG 346 (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 TYR* 4.6 10.7 + - - +
342A LEU 2.9 18.4 + - - +
343A GLY* 4.0 3.8 - - - +
345A ALA* 1.4 72.2 - - - +
347A LYS* 1.3 64.2 + - - +
348A ILE 3.5 0.2 + - - -
349A TYR* 3.7 19.4 + - - +
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Residues in contact with LYS 347 (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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10A TYR* 3.8 38.8 - - + -
11A ALA* 5.1 4.9 - - - +
14A LYS* 6.6 0.2 - - - -
57A LYS* 4.4 19.1 + - - +
59A ASN* 2.9 41.3 + - - +
62A LEU* 5.6 2.2 - - - -
343A GLY 3.1 15.3 + - - +
344A LEU* 3.1 15.9 + - + +
346A ARG* 1.3 77.6 - - - +
348A ILE* 1.4 59.5 + - + +
349A TYR 4.8 1.0 - - - +
351A ARG* 5.0 5.4 - - - +
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Residues in contact with ILE 348 (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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59A ASN* 4.2 13.5 - - - +
206A PHE* 4.0 21.3 - - + -
235A MET* 3.9 23.3 - - + +
238A PHE* 3.6 29.6 - - + -
239A PHE* 3.7 29.8 - - + -
242A GLN* 2.9 24.7 - - - +
325A ILE* 6.1 0.2 - - + -
344A LEU* 3.1 21.5 + - + +
345A ALA* 3.4 14.4 - - - +
347A LYS* 1.4 79.6 - - - +
349A TYR* 1.3 62.2 + - - +
351A ARG* 3.1 16.3 - - - +
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Residues in contact with TYR 349 (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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238A PHE* 4.6 7.6 - - + -
242A GLN* 4.5 1.6 - - - -
318A GLU* 4.6 0.9 - - + -
322A TYR* 3.6 30.1 - - + +
345A ALA 2.9 17.3 + - - +
346A ARG* 4.0 14.3 - - - +
347A LYS 3.7 2.2 - - - +
348A ILE* 1.3 77.6 - - - +
350A LYS* 1.4 71.6 + - + +
351A ARG* 3.2 1.8 + - - -
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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