Contacts of the helix formed by residues 313 - 332 (chain C) in PDB entry 4KYI
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 ALA 313 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312C GLU* 1.3 74.6 - - - +
314C GLY* 1.3 55.6 + - - +
315C THR* 4.0 15.7 - - + +
316C ALA* 2.9 12.2 + - + +
317C PHE* 2.5 35.2 + - - +
376C THR* 3.4 6.9 + - - -
377C GLY 5.4 0.2 - - - -
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Residues in contact with GLY 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C GLU 3.7 1.4 + - - -
313C ALA* 1.3 71.4 - - - +
315C THR* 1.3 61.5 + - - +
317C PHE* 4.1 1.8 - - - -
318C GLU* 3.1 38.1 + - - +
375C ASN* 3.4 24.6 + - - -
376C THR* 4.1 2.2 + - - -
377C GLY* 4.4 10.2 + - - -
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Residues in contact with THR 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313C ALA* 4.0 10.3 - - + +
314C GLY* 1.3 76.1 - - - +
316C ALA* 1.3 62.3 + - - +
318C GLU* 4.7 4.1 - - - +
319C ASP* 3.1 27.0 + - - +
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Residues in contact with ALA 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C GLU* 3.8 14.3 - - + +
313C ALA* 2.9 22.7 + - + +
315C THR* 1.3 80.5 + - - +
317C PHE* 1.3 66.0 + - - +
319C ASP* 4.0 5.4 - - - +
320C ARG* 3.4 20.3 + - - +
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Residues in contact with PHE 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C GLU* 3.8 7.2 + - + +
313C ALA 2.5 20.1 + - - +
314C GLY 3.3 4.2 + - - +
316C ALA* 1.3 71.7 - - - +
318C GLU* 1.3 73.1 + - + +
320C ARG* 3.3 34.4 + - - +
321C VAL* 3.3 34.8 + - + +
373C TYR* 3.4 25.1 - - + -
374C ILE 4.4 1.3 - - - -
375C ASN* 3.2 51.4 - - + -
397C ASN* 4.9 2.9 - - - -
401C GLN* 3.2 31.2 - - - -
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Residues in contact with GLU 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314C GLY* 3.1 20.3 + - - +
315C THR* 4.7 4.0 - - - +
317C PHE* 1.3 85.3 - - + +
319C ASP* 1.3 57.7 + - - +
321C VAL* 3.2 5.3 + - - +
322C ASN* 2.8 53.7 + - - +
375C ASN* 4.9 6.0 + - - +
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Residues in contact with ASP 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315C THR 3.1 20.3 + - - +
316C ALA* 4.0 7.4 - - - +
317C PHE 3.3 0.8 - - - -
318C GLU* 1.3 78.7 - - - +
320C ARG* 1.3 58.7 + - - +
322C ASN* 4.2 7.7 - - - +
323C LYS* 3.2 36.9 + - - +
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Residues in contact with ARG 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C GLU* 2.2 38.8 + - - +
316C ALA 3.4 8.5 + - - +
317C PHE* 3.3 30.4 + - - +
318C GLU 3.1 0.2 - - - -
319C ASP* 1.3 78.9 - - - +
321C VAL* 1.3 79.3 + - - +
323C LYS* 3.6 16.9 + - - +
324C ALA* 3.4 18.5 + - - +
373C TYR* 3.2 54.3 - - - +
401C GLN* 5.1 2.8 - - - +
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Residues in contact with VAL 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317C PHE* 3.3 32.1 - - + +
318C GLU* 3.2 7.3 + - - +
320C ARG* 1.3 96.1 - - - +
322C ASN* 1.3 69.2 + - - +
324C ALA* 2.9 17.4 + - + +
325C LYS* 3.0 45.3 + - + +
401C GLN* 5.4 3.1 - - - +
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Residues in contact with ASN 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318C GLU* 2.8 45.3 + - - +
319C ASP* 4.1 8.4 - - - +
321C VAL* 1.3 75.5 - - - +
323C LYS* 1.3 58.9 + - + +
325C LYS* 3.7 5.5 + - - +
326C GLN* 3.1 31.2 + - - +
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Residues in contact with LYS 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C ASP* 3.2 30.5 + - - +
320C ARG* 3.9 16.6 + - - +
321C VAL 3.2 0.6 - - - -
322C ASN* 1.3 75.1 - - + +
324C ALA* 1.3 55.5 + - - +
326C GLN* 3.5 13.9 - - - +
327C SER* 2.7 35.6 + - - -
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Residues in contact with ALA 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320C ARG 3.4 11.2 + - - +
321C VAL* 2.9 12.2 + - - +
323C LYS* 1.3 77.5 - - - +
325C LYS* 1.3 72.5 + - + +
327C SER* 3.1 16.3 + - - -
328C ALA* 3.2 14.2 + - - +
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Residues in contact with LYS 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321C VAL* 3.0 42.3 + - + +
322C ASN* 4.1 6.1 - - - +
324C ALA* 1.3 82.3 - - + +
326C GLN* 1.3 58.2 + - - +
328C ALA* 3.6 5.1 + - - +
329C MET* 3.1 30.1 + - + +
404C GLN* 4.9 12.1 - - - +
557C LYS* 5.7 0.3 + - - -
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Residues in contact with GLN 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322C ASN* 3.1 22.4 + - - +
323C LYS* 3.6 12.7 - - - +
324C ALA 3.2 0.2 - - - -
325C LYS* 1.3 75.1 - - - +
327C SER* 1.3 65.9 + - - +
329C MET* 3.2 22.3 + - + +
330C GLU* 3.1 45.0 + - + +
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Residues in contact with SER 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323C LYS 2.7 20.7 + - - -
324C ALA* 3.3 11.2 - - - -
326C GLN* 1.3 74.8 - - - +
328C ALA* 1.3 61.3 + - - +
330C GLU* 3.1 20.1 + - - +
331C ALA* 3.4 10.4 + - - +
361C ARG* 4.4 18.7 + - - +
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Residues in contact with ALA 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324C ALA 3.2 11.3 + - - +
325C LYS* 4.1 5.2 - - - +
327C SER* 1.3 79.0 + - - +
329C MET* 1.3 61.0 + - - +
331C ALA* 3.4 17.6 + - - +
332C ILE* 3.6 20.2 - - - +
543C GLU* 4.0 27.4 - - + +
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Residues in contact with MET 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325C LYS* 3.1 16.7 + - + +
326C GLN* 3.4 29.4 - - + +
327C SER 3.1 0.2 - - - -
328C ALA* 1.3 79.3 - - - +
330C GLU* 1.3 60.3 + - + +
332C ILE* 3.9 7.1 + - - +
333C SER* 3.5 18.0 + - - -
557C LYS* 3.8 32.8 - - - +
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Residues in contact with GLU 330 (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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326C GLN* 3.3 37.4 + - + +
327C SER* 3.1 10.6 + - - +
329C MET* 1.3 78.3 - - + +
331C ALA* 1.3 63.0 + - - +
332C ILE 3.1 2.5 - - - -
333C SER* 3.9 8.3 - - - -
334C TRP* 3.0 47.0 + - + +
361C ARG* 3.8 21.3 + - - +
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Residues in contact with ALA 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327C SER 3.4 8.4 + - - +
328C ALA* 3.4 15.6 + - - +
330C GLU* 1.3 77.2 - - - +
332C ILE* 1.3 61.6 + - + +
334C TRP* 4.4 5.7 - - - +
335C PHE* 3.9 14.6 + - - +
539C TRP 4.1 7.6 - - - +
541C PRO* 4.2 18.1 - - + +
542C ILE* 5.3 8.7 - - + +
543C GLU* 5.3 8.1 - - + +
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Residues in contact with ILE 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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328C ALA 3.6 17.9 + - - +
329C MET* 3.9 5.8 + - - +
330C GLU 3.1 0.6 - - - -
331C ALA* 1.3 78.0 - - + +
333C SER* 1.3 63.5 + - - +
334C TRP 3.4 0.7 - - - -
335C PHE* 3.6 12.8 - - + +
336C LYS* 3.3 27.6 + - + +
541C PRO* 4.2 25.8 - - + -
543C GLU* 6.0 4.3 - - + -
553C ALA 6.1 0.9 - - - +
554C GLN* 6.3 1.1 - - - -
555C ASP* 4.3 31.9 - - + +
556C PHE 5.7 3.4 - - - -
557C LYS* 5.7 10.8 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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