Contacts of the helix formed by residues 333 - 342 (chain K) in PDB entry 6X5A
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 GLY 333 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328K ILE* 3.6 5.5 + - - +
329K GLN* 3.2 26.1 + - - +
332K LEU* 1.3 80.7 - - - +
334K THR* 1.3 64.2 + - - -
335K LYS* 3.4 6.5 - - - -
336K VAL* 3.4 19.2 - - - +
337K ARG* 3.7 1.6 + - - +
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Residues in contact with THR 334 (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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130I A 5.5 6.4 + - - +
329K GLN* 3.4 31.7 + - - -
333K GLY* 1.3 72.7 - - - -
335K LYS* 1.3 65.2 + - + +
337K ARG* 3.3 0.9 + - - +
338K THR* 2.9 32.5 + - - +
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Residues in contact with LYS 335 (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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332K LEU* 6.4 0.4 - - - -
333K GLY* 5.1 4.3 - - - -
334K THR* 1.3 83.4 - - + +
336K VAL* 1.3 85.7 + - - +
338K THR* 3.0 12.5 - - + +
339K ASN* 3.0 24.8 + - + +
382K LYS* 4.6 15.7 - - - +
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Residues in contact with VAL 336 (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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328K ILE* 3.6 18.4 - - + -
332K LEU* 3.7 22.4 - - + -
333K GLY* 3.4 16.1 + - - +
335K LYS* 1.3 96.3 - - + +
337K ARG* 1.3 58.6 + - - +
339K ASN* 3.1 6.2 + - + -
340K LEU* 2.5 43.6 + - + +
373K TYR* 3.7 35.2 - - + +
382K LYS* 3.8 12.6 - - - +
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Residues in contact with ARG 337 (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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323K LYS 3.4 19.0 + - - -
324K GLU* 4.2 10.9 + - - +
325K GLY 2.4 25.1 + - - +
326K LEU* 2.8 28.2 + - + +
327K PRO* 4.5 1.2 - - - +
328K ILE* 3.8 16.4 - - + -
329K GLN* 3.1 49.0 - - - +
333K GLY 3.7 0.4 + - - +
334K THR 3.3 3.9 + - - +
336K VAL* 1.3 81.3 - - - +
338K THR* 1.3 58.4 + - - +
340K LEU* 4.2 4.7 - - - -
341K ARG* 2.8 78.5 + - + +
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Residues in contact with THR 338 (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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76G THR* 5.4 2.9 + - - +
51H ASP* 6.1 1.2 - - - +
329K GLN* 5.5 0.4 - - - +
334K THR* 2.9 19.3 + - - +
335K LYS* 3.0 21.5 - - + +
337K ARG* 1.3 75.5 - - - +
339K ASN* 1.3 64.4 + - + +
341K ARG* 3.3 4.1 + - - +
342K ARG* 2.9 50.6 + - - +
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Residues in contact with ASN 339 (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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74G LYS* 3.4 32.1 + - - +
335K LYS* 3.0 15.0 + - + +
336K VAL* 3.5 7.2 - - + +
338K THR* 1.3 82.5 - - + +
340K LEU* 1.3 66.9 + - - +
342K ARG* 3.2 19.6 + - - +
343K GLU* 3.5 12.5 + - - +
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Residues in contact with LEU 340 (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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318K TRP* 3.6 6.1 - - + -
326K LEU* 3.6 24.2 - - + -
328K ILE* 5.1 10.1 - - + -
336K VAL* 2.5 26.6 + - + +
337K ARG* 3.8 4.0 - - - +
339K ASN* 1.3 75.6 + - - +
341K ARG* 1.3 56.3 + - - +
343K GLU* 3.0 53.5 + - - +
370K THR* 3.1 36.8 - - - +
373K TYR* 4.6 26.0 - - + -
374K ILE* 5.7 5.4 - - + -
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Residues in contact with ARG 341 (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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71G ARG* 3.7 10.4 + - - -
51H ASP* 3.9 22.5 + - - +
317K SER 5.7 0.4 + - - -
318K TRP* 3.5 56.1 + - + +
322K THR* 3.3 43.0 + - - +
323K LYS* 3.4 14.1 + - - +
325K GLY 4.3 2.4 + - - -
326K LEU* 4.5 6.4 - - + +
337K ARG* 2.8 73.2 + - + +
338K THR* 3.6 5.2 - - - +
340K LEU* 1.3 69.9 - - - +
342K ARG* 1.3 58.1 + - - +
343K GLU 3.2 4.3 + - - +
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Residues in contact with ARG 342 (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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71G ARG* 3.1 70.7 + - - +
74G LYS* 3.1 22.5 - - + +
75G LYS 2.5 50.2 + - - +
76G THR* 4.5 9.5 + - - +
51H ASP* 6.6 0.2 - - - -
52H THR* 6.2 2.2 - - - +
338K THR* 2.9 36.7 + - - +
339K ASN* 3.4 10.3 - - - +
340K LEU 3.1 0.6 - - - -
341K ARG* 1.3 76.5 - - - +
343K GLU* 1.3 63.4 + - - +
344K PRO* 4.5 1.0 - - - +
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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