Contacts of the helix formed by residues 351 - 363 (chain K) in PDB entry 5ANC
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 ILE 351 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38K CYS* 3.9 29.4 - - - +
39K LEU* 5.0 10.8 - - + -
42K SER* 4.3 9.2 + - - +
242K GLY* 3.2 35.9 - - - +
243K PHE* 5.3 0.4 - - - -
246K GLU* 5.5 5.6 - - - +
348K TRP 5.4 0.7 - - - +
349K LEU* 2.6 18.0 + - + +
350K PRO* 1.3 67.0 - - - +
352K SER* 1.3 57.3 + - - +
353K HIS* 3.1 9.6 - - + -
354K ALA* 2.9 11.2 + - + -
355K VAL* 2.7 62.4 + - + +
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Residues in contact with SER 352 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1K MET* 5.2 11.2 - - - +
42K SER* 2.7 24.2 + - - -
79K TYR* 3.5 20.3 - - - -
81K THR* 4.0 15.2 + - - +
350K PRO* 3.2 3.7 - - - -
351K ILE* 1.3 78.9 - - - +
353K HIS* 1.3 61.6 + - - +
355K VAL* 4.3 2.9 - - - -
356K LEU* 3.1 49.2 - - - +
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Residues in contact with HIS 353 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81K THR* 5.3 2.7 - - - +
250K ARG* 3.4 38.7 + - - -
347K GLN 6.0 0.7 - - - -
348K TRP 4.5 10.8 - - - -
350K PRO* 2.7 31.3 + - - +
351K ILE* 3.1 2.4 + - - -
352K SER* 1.3 78.3 - - - +
354K ALA* 1.3 81.1 + - + +
357K ALA* 4.7 9.2 + - - +
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Residues in contact with ALA 354 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246K GLU* 4.3 22.2 - - + +
250K ARG* 4.5 10.1 - - - +
351K ILE* 2.9 9.7 + - + +
353K HIS* 1.3 100.0 - - + +
355K VAL* 1.3 63.3 + - + +
356K LEU 3.4 2.1 + - - -
357K ALA* 3.5 12.3 + - - +
358K MET* 3.5 22.2 + - + +
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Residues in contact with VAL 355 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231K ASN* 3.7 22.4 - - - +
233K VAL* 5.9 4.3 - - + -
246K GLU* 5.4 10.1 - - - +
351K ILE* 2.7 55.5 + - + +
352K SER* 4.3 4.5 - - - +
354K ALA* 1.3 72.8 - - + +
356K LEU* 1.3 69.3 + - + +
358K MET* 3.2 8.0 + - + +
359K VAL* 2.9 35.7 + - + +
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Residues in contact with LEU 356 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79K TYR* 5.1 4.3 - - + -
81K THR* 3.5 37.2 - - + +
86K TYR* 3.7 57.1 + - + +
88K ILE* 5.1 10.8 - - + -
352K SER* 3.1 37.8 + - - +
353K HIS 5.5 0.2 - - - +
354K ALA 3.4 0.8 - - - -
355K VAL* 1.3 87.3 - - + +
357K ALA* 1.3 57.8 + - - +
359K VAL* 3.2 11.1 + - + +
360K CYS* 2.9 28.6 + - - +
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Residues in contact with ALA 357 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353K HIS 4.7 7.7 + - - +
354K ALA 3.5 12.4 + - - +
355K VAL 3.2 0.6 - - - -
356K LEU* 1.3 77.3 - - - +
358K MET* 1.3 62.8 + - + +
360K CYS* 3.2 9.3 + - - +
361K GLN* 2.9 39.4 + - + +
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Residues in contact with MET 358 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228K GLU 4.8 0.7 - - - +
229K GLN 3.7 15.1 - - - +
230K GLY* 3.2 33.0 - - - +
231K ASN* 4.2 11.4 - - + +
246K GLU* 4.1 20.4 - - + -
260K LYS* 5.6 9.0 - - + -
264K MET* 4.0 22.0 - - + -
354K ALA* 3.5 17.5 - - + +
355K VAL* 3.2 13.1 + - + +
357K ALA* 1.3 81.6 - - + +
359K VAL* 1.3 56.3 + - - +
361K GLN* 3.2 23.1 + - - +
362K LYS* 2.9 29.2 + - - +
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Residues in contact with VAL 359 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20K ARG* 4.1 18.4 - - + +
22K ILE* 3.4 41.1 - - + -
86K TYR* 5.0 6.7 - - + -
88K ILE* 6.6 0.4 - - + -
231K ASN* 3.9 19.3 - - - +
355K VAL* 2.9 28.4 + - + +
356K LEU* 3.2 14.1 + - + +
358K MET* 1.3 77.0 - - - +
360K CYS* 1.3 57.6 + - - +
362K LYS* 3.2 9.9 + - - +
363K LEU* 2.9 30.8 + - + +
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Residues in contact with CYS 360 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20K ARG* 3.3 42.6 - - - +
84K GLU* 5.1 1.8 - - - -
86K TYR* 4.8 0.4 - - - +
356K LEU 2.9 11.2 + - - +
357K ALA* 3.3 12.3 - - - +
359K VAL* 1.3 77.1 - - - +
361K GLN* 1.3 63.7 + - + +
363K LEU 3.0 24.3 - - - +
364K PRO* 3.7 5.7 - - - +
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Residues in contact with GLN 361 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229K GLN* 3.0 46.3 + - + +
261K GLU* 4.2 17.0 + - - +
357K ALA* 2.9 20.2 + - + +
358K MET* 3.2 33.5 + - - +
360K CYS* 1.3 78.7 - - + +
362K LYS* 1.3 63.2 - - - +
363K LEU 4.9 0.5 - - - -
364K PRO* 4.9 2.6 - - - +
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Residues in contact with LYS 362 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22K ILE* 4.6 10.8 - - - +
112K GLY* 4.5 14.1 + - - -
114K ILE* 5.1 2.0 - - - +
139K ILE 5.4 0.6 + - - -
140K ARG* 2.5 79.4 + - + +
141K PRO* 5.0 0.4 - - - +
142K VAL* 4.1 14.4 - - + +
228K GLU* 4.0 28.5 - - + +
229K GLN* 4.1 7.0 - - - +
231K ASN* 4.1 23.5 - - - +
358K MET 2.9 13.3 + - - +
359K VAL* 3.2 10.5 + - - +
361K GLN* 1.3 79.6 - - - +
363K LEU* 1.3 73.8 + - - +
364K PRO* 3.7 7.7 - - - +
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Residues in contact with LEU 363 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20K ARG* 3.2 40.2 - - + +
21K ASN* 3.9 22.4 - - + +
22K ILE* 4.5 8.3 - - + -
112K GLY* 5.2 2.9 - - - -
139K ILE 5.0 0.4 - - - +
140K ARG* 4.6 11.9 - - + -
359K VAL 2.9 12.0 + - - +
360K CYS 3.0 11.9 - - - +
362K LYS* 1.3 89.0 - - - +
364K PRO* 1.4 69.5 - - + +
365K SER 3.9 17.9 - - - +
366K PRO* 5.0 1.3 - - + -
369K ILE* 3.6 44.0 - - + -
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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