Contacts of the helix formed by residues 331 - 342 (chain C) in PDB entry 5KKR
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163C GLU* 2.4 32.7 + - - -
329C VAL 4.1 0.8 + - - -
330C PHE* 1.3 77.6 - - - +
332C LEU* 1.3 64.5 + - - +
333C GLU* 3.0 26.2 + - - -
334C PHE* 3.2 8.5 + - - -
335C GLN* 3.1 19.4 + - - +
363C ARG* 3.4 7.7 + - - -
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Residues in contact with LEU 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327C SER* 5.9 1.3 - - - +
328C ALA 6.0 0.9 - - - +
330C PHE 5.0 0.7 - - - +
331C SER* 1.3 73.9 - - - +
333C GLU* 1.3 59.7 + - + +
335C GLN* 3.7 28.3 - - + +
336C ASP* 3.0 30.5 + - - +
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Residues in contact with GLU 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331C SER* 3.0 14.5 + - - +
332C LEU* 1.3 81.2 + - + +
334C PHE* 1.3 56.5 + - - +
336C ASP* 4.8 1.1 - - - -
337C PHE 3.1 20.8 + - - -
358C HIS* 3.2 17.2 - - - -
359C ALA* 4.4 19.7 - - + +
360C PHE* 3.3 26.0 - - + +
363C ARG* 2.4 43.2 + - - +
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Residues in contact with PHE 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163C GLU* 3.2 34.5 - - + +
166C LEU* 3.7 34.8 - - + -
253C LEU* 4.5 19.7 - - + -
257C ALA* 4.3 2.5 - - + -
325C LEU* 3.5 30.2 - - + +
330C PHE* 3.7 23.8 - + + -
331C SER* 3.2 6.2 + - - +
333C GLU* 1.3 76.9 - - - +
335C GLN* 1.3 65.9 + - - +
337C PHE* 3.4 8.8 + + + -
338C VAL* 3.4 26.5 + - + -
360C PHE* 3.4 39.2 - + + -
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Residues in contact with GLN 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325C LEU* 4.1 21.8 - - + +
326C PRO 3.4 20.6 + - - -
327C SER* 3.4 18.9 + - - +
328C ALA 3.6 4.0 - - - +
330C PHE* 2.8 31.1 + - + +
331C SER 3.1 14.1 + - - +
332C LEU* 3.7 26.3 - - - +
333C GLU 3.3 0.2 - - - -
334C PHE* 1.3 77.2 - - - +
336C ASP* 1.3 56.3 + - - +
338C VAL* 3.3 9.5 - - - +
339C ASN* 2.6 35.4 + - - +
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Residues in contact with ASP 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332C LEU 3.0 18.8 + - - +
333C GLU* 3.9 2.0 - - - +
335C GLN* 1.3 74.9 - - - +
337C PHE* 1.3 65.7 + - - +
339C ASN* 3.3 10.3 + - - +
340C LYS* 3.1 46.9 + - - +
358C HIS* 2.7 24.6 + - + +
359C ALA* 6.0 0.2 - - - +
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Residues in contact with PHE 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C SER* 4.1 11.9 - - - -
174C ILE* 4.6 4.9 - - + -
249C MET* 4.2 22.2 - - + -
253C LEU* 3.6 31.2 - - + -
333C GLU 3.1 18.0 + - - +
334C PHE* 3.5 6.7 - + - +
335C GLN 3.2 0.6 - - - -
336C ASP* 1.3 79.1 - - - +
338C VAL* 1.3 66.9 + - + +
340C LYS* 3.4 8.3 + - - +
341C CYS* 3.3 21.2 - - - -
355C LEU* 3.9 22.9 - - + -
358C HIS* 3.5 27.6 - + + -
360C PHE* 3.7 20.9 - + + -
361C ILE* 3.5 32.8 - - + -
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Residues in contact with VAL 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250C GLY* 4.5 6.5 - - - +
253C LEU* 4.2 19.7 - - + -
254C VAL* 4.4 14.1 - - + -
324C LYS* 5.7 0.2 - - - -
325C LEU* 3.6 33.9 - - + +
334C PHE* 3.4 30.3 + - + +
335C GLN 3.3 13.2 - - - +
337C PHE* 1.3 81.0 - - + +
339C ASN* 1.3 68.0 + - - +
341C CYS* 3.3 7.3 + - - +
342C LEU* 3.0 35.1 + - + +
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Residues in contact with ASN 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323C PRO 4.2 14.0 - - - +
324C LYS* 4.4 11.5 - - - +
325C LEU 4.8 2.3 + - - +
335C GLN* 2.6 33.3 + - - +
336C ASP* 3.3 12.0 + - - +
337C PHE 3.2 1.0 - - - -
338C VAL* 1.3 82.5 - - - +
340C LYS* 1.3 62.9 + - + +
341C CYS 3.1 2.5 + - - -
342C LEU* 3.6 8.1 + - - +
343C ILE* 3.2 19.8 + - - +
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Residues in contact with LYS 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336C ASP* 3.1 45.6 + - - +
337C PHE* 3.7 6.5 - - - +
338C VAL 3.3 0.4 - - - -
339C ASN* 1.3 78.0 - - - +
341C CYS* 1.3 59.1 + - - +
343C ILE* 3.7 18.5 - - + +
349C ARG* 3.5 4.5 - - - +
350C ALA* 3.2 41.4 + - + +
355C LEU* 4.8 4.9 - - + -
358C HIS* 4.7 13.1 - - + +
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Residues in contact with CYS 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246C ILE* 3.7 39.0 - - + +
247C TRP* 3.8 10.7 - - - -
249C MET* 3.8 15.9 - - - -
250C GLY* 4.0 10.5 - - - -
337C PHE* 3.3 23.8 - - - -
338C VAL* 3.3 8.2 + - - +
339C ASN 3.1 0.6 - - - -
340C LYS* 1.3 77.1 - - - +
342C LEU* 1.3 57.1 + - - +
343C ILE 3.2 9.2 + - - -
349C ARG* 3.3 21.2 + - - -
355C LEU* 3.7 18.2 - - - -
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Residues in contact with LEU 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247C TRP* 3.2 38.2 - - + +
250C GLY 3.9 4.0 - - - +
251C LEU* 3.4 32.3 - - + +
254C VAL* 4.0 21.1 - - + -
322C PRO* 3.2 31.8 - - + +
323C PRO* 3.5 40.4 - - + +
338C VAL* 3.0 21.9 + - + +
339C ASN* 3.6 7.3 + - - +
340C LYS 3.6 0.2 - - - -
341C CYS* 1.3 75.6 - - - +
343C ILE* 1.3 59.5 + - - +
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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