Contacts of the helix formed by residues 331 - 340 (chain K) in PDB entry 3HX0
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 SER 331 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270K GLN* 5.8 1.1 - - - -
329K SER* 3.2 14.1 + - - -
330K GLU* 1.3 81.5 - - - +
332K VAL* 1.3 67.0 + - - +
334K VAL* 2.8 7.1 + - - +
335K LEU* 2.8 38.2 + - - -
353K TYR* 3.1 39.7 + - - -
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Residues in contact with VAL 332 (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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262K VAL* 5.8 1.1 - - + +
265K LYS 5.0 1.3 - - - +
266K ALA* 4.2 29.2 - - + +
269K VAL* 4.3 8.7 - - + +
270K GLN* 4.4 17.9 - - - +
328K ILE* 3.3 31.6 - - + -
329K SER* 3.7 6.0 + - - +
331K SER* 1.3 76.0 - - - +
333K PRO* 1.3 63.0 - - + +
335K LEU* 3.7 7.0 - - - +
336K GLU* 2.7 48.6 + - + +
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Residues in contact with PRO 333 (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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329K SER 4.6 1.8 - - - +
330K GLU* 3.2 20.6 - - - +
332K VAL* 1.3 97.4 - - + +
334K VAL* 1.3 59.2 + - + +
336K GLU* 3.7 7.3 - - + +
337K LEU* 2.8 33.2 + - - +
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Residues in contact with VAL 334 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330K GLU 4.7 6.7 - - - +
331K SER 2.8 7.4 + - - +
333K PRO* 1.3 74.3 - - + +
335K LEU* 1.3 60.7 + - - +
337K LEU* 3.3 8.0 + - - +
338K PHE* 3.0 55.5 + - + -
353K TYR* 3.4 34.3 - - + +
357K PHE 3.9 7.4 - - - +
358K ARG* 3.6 35.9 - - + +
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Residues in contact with LEU 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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269K VAL* 4.0 24.9 - - + +
270K GLN* 4.4 20.9 - - + +
331K SER* 2.8 39.2 + - - +
332K VAL* 3.7 5.2 - - - +
334K VAL* 1.3 74.0 - - - +
336K GLU* 1.3 56.3 + - - +
338K PHE* 3.3 4.2 + - + +
339K SER* 2.8 30.4 + - - -
349K ALA* 3.7 38.6 - - + +
350K GLN* 3.7 19.7 - - + +
353K TYR* 4.2 13.7 - - + -
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Residues in contact with GLU 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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265K LYS* 4.3 25.9 - - - +
269K VAL* 3.9 18.2 - - + +
332K VAL* 2.7 30.3 + - + +
333K PRO* 3.8 6.6 - - - +
335K LEU* 1.3 70.0 - - - +
337K LEU* 1.3 61.9 + - - +
339K SER* 2.6 24.3 + - - +
340K ASN* 2.6 37.8 + - - +
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Residues in contact with LEU 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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333K PRO 2.8 18.6 + - - +
334K VAL* 3.4 6.3 - - - +
336K GLU* 1.3 77.7 - - - +
338K PHE* 1.3 69.4 + - + +
340K ASN* 3.5 5.3 + - - +
358K ARG 4.4 10.3 - - - +
359K SER* 4.6 1.1 - - - +
360K LEU* 3.6 41.4 - - + +
380K TYR* 3.0 57.9 + - + +
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Residues in contact with PHE 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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334K VAL* 3.0 37.7 + - + +
335K LEU* 3.6 4.3 - - - +
337K LEU* 1.3 80.0 - - + +
339K SER* 1.3 65.6 + - - +
340K ASN 3.1 2.2 - - - -
341K ILE* 2.9 30.4 + - + +
344K ALA* 3.5 6.9 - - - +
349K ALA* 3.9 20.6 - - + -
352K TRP* 3.5 43.5 - + + -
353K TYR* 4.3 2.9 - - + -
357K PHE 3.6 30.7 - - - -
358K ARG 4.0 4.5 - - - -
359K SER 4.0 15.5 - - - -
360K LEU* 4.1 10.3 - - + -
363K ILE* 3.9 24.0 - - + -
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Residues in contact with SER 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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269K VAL* 3.7 19.4 - - - +
335K LEU 2.8 17.6 + - - -
336K GLU* 2.6 29.7 + - - +
338K PHE* 1.3 73.6 - - - +
340K ASN* 1.3 57.5 + - - +
341K ILE 2.9 2.1 + - - -
344K ALA 3.1 11.6 - - - +
345K GLY* 5.0 9.4 - - - -
346K THR* 5.3 1.3 - - - -
349K ALA* 4.6 4.9 - - - +
807K NA 2.3 32.2 - - - -
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Residues in contact with ASN 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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336K GLU* 2.6 45.5 + - - +
337K LEU* 3.6 2.5 - - - +
338K PHE 3.1 0.8 - - - -
339K SER* 1.3 78.1 + - - +
341K ILE* 1.3 59.4 + - - +
342K TRP* 3.6 2.1 + - - -
376K GLY 5.3 0.3 - - - +
380K TYR* 3.3 36.5 + - + +
383K PHE* 5.9 3.3 - - - +
384K LEU* 4.5 25.7 - - + +
807K NA 4.4 0.7 - - - -
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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