Contacts of the helix formed by residues 321 - 335 (chain C) in PDB entry 4K2S
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 321 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C PHE* 3.5 31.3 - - - -
21C THR* 5.0 1.6 + - - -
35C ASP* 3.0 31.6 + - - -
319C ASP 4.0 0.2 - - - -
320C LEU* 1.3 76.5 - - - +
322C PRO* 1.3 75.0 - - - +
323C VAL* 3.1 23.4 + - - +
324C CYS* 3.0 11.4 + - - +
325C LEU* 3.0 9.7 + - - +
346C HIS* 3.9 0.9 - - - -
354C PHE* 4.4 6.7 - - - -
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Residues in contact with PRO 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C PHE* 4.7 0.2 - - + -
321C SER* 1.3 88.9 - - - +
323C VAL* 1.3 55.5 + - - +
324C CYS 3.3 0.2 - - - -
325C LEU* 3.6 5.2 - - + -
326C GLY 2.8 25.5 + - - -
346C HIS* 3.7 15.7 - - + +
350C THR* 3.7 32.1 - - + -
351C ASP* 4.4 7.0 - - - +
354C PHE* 3.6 36.1 - - + +
356C HIS* 4.5 0.9 - - - +
358C TYR* 3.4 22.1 - - + +
375C VAL* 3.4 11.8 - - + +
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Residues in contact with VAL 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C THR* 4.6 7.6 - - + +
33C ILE* 3.7 33.7 - - + +
34C GLY* 3.9 1.1 - - - -
35C ASP 3.8 17.9 - - - +
93C MET* 4.7 2.7 - - - -
321C SER* 3.0 13.8 - - - +
322C PRO* 1.3 77.5 - - - +
324C CYS* 1.3 62.8 + - - +
326C GLY* 3.5 0.7 + - - -
327C ALA* 3.2 22.9 + - - +
354C PHE* 3.7 26.7 - - + -
373C HIS* 3.6 27.8 - - + +
375C VAL* 3.8 11.4 - - + +
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Residues in contact with CYS 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C ASP* 3.5 9.4 - - + +
93C MET* 4.1 9.6 - - - -
288C PRO* 4.6 2.2 - - - -
289C LEU* 4.1 14.3 - - - +
290C THR* 3.1 41.7 - - - +
315C HIS 5.5 0.4 - - - -
320C LEU* 4.0 23.8 - - + -
321C SER* 3.0 11.0 + - - +
323C VAL* 1.3 79.9 - - - +
325C LEU* 1.3 57.4 + - - +
327C ALA* 3.4 1.7 + - - +
328C ALA* 2.8 37.7 + - - +
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Residues in contact with LEU 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316C GLY* 5.7 4.9 - - - +
320C LEU* 5.5 1.3 - - + +
321C SER 3.0 12.2 + - - +
322C PRO* 3.2 8.2 + - + +
324C CYS* 1.3 76.3 - - - +
326C GLY* 1.3 59.0 + - - +
328C ALA* 3.2 4.1 + - + +
329C ILE* 2.9 54.4 + - + +
341C GLN* 4.1 20.4 - - - +
342C GLU 4.9 3.8 - - - +
343C HIS* 4.8 8.3 - - + +
344C MET 5.6 1.3 - - - +
346C HIS* 4.1 20.0 - - + +
358C TYR* 3.6 27.1 - - + +
365C PHE* 3.9 23.1 - - + -
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Residues in contact with GLY 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322C PRO 2.8 16.7 + - - -
325C LEU* 1.3 76.0 - - - +
327C ALA* 1.3 60.9 + - - +
329C ILE* 3.3 3.9 + - - +
330C HIS* 3.2 26.7 + - - -
358C TYR* 3.4 28.0 - - - +
373C HIS 4.0 8.5 - - - -
375C VAL* 3.7 10.5 - - - -
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Residues in contact with ALA 327 (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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93C MET* 4.3 16.4 - - + -
107C LEU* 4.4 10.7 - - + +
289C LEU* 3.6 18.2 - - + +
295C ILE* 4.4 4.2 - - + +
323C VAL 3.2 16.8 + - - +
324C CYS 3.8 0.9 - - - +
326C GLY* 1.3 74.7 - - - +
328C ALA* 1.3 56.9 + - - +
330C HIS* 3.3 4.0 + - - +
331C PHE* 2.9 28.2 + - - +
373C HIS* 4.0 26.4 - - + +
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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
----------------------------------------------------------
289C LEU* 3.5 13.6 - - + +
314C PHE* 4.0 20.6 - - + -
324C CYS* 2.8 24.7 + - - +
325C LEU* 3.2 7.2 + - + +
327C ALA* 1.3 74.7 - - - +
329C ILE* 1.3 56.1 + - - +
331C PHE* 3.3 4.1 + - - +
332C ASP* 2.7 41.7 + - - +
341C GLN* 4.1 12.8 - - - +
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Residues in contact with ILE 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C VAL* 4.5 4.5 - - + -
325C LEU* 2.9 33.3 + - + +
326C GLY 3.7 4.3 - - - +
328C ALA* 1.3 73.9 - - - +
330C HIS* 1.3 59.8 + - + +
332C ASP* 3.4 12.5 + - - +
333C THR* 2.6 36.0 + - - +
341C GLN* 5.1 0.7 - - + -
358C TYR* 3.6 26.7 - - + -
365C PHE* 3.4 53.8 - - + -
366C LEU 4.0 1.3 - - - +
367C ALA* 3.6 32.3 - - + +
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Residues in contact with HIS 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C PRO* 3.6 7.0 - - + -
107C LEU* 3.6 28.7 - - + -
108C TYR* 3.1 42.0 + + - +
111C LEU* 4.5 2.0 - - - -
326C GLY 3.2 23.5 + - - -
327C ALA 3.5 7.2 - - - +
329C ILE* 1.3 77.7 - - + +
331C PHE* 1.3 61.3 + - - +
333C THR* 3.1 10.3 + - - -
334C TRP* 3.2 10.9 + - - +
367C ALA* 4.2 1.5 - - + +
368C GLY* 3.3 40.4 + - - -
370C SER 4.9 0.6 + - - -
372C GLY 3.9 0.6 + - - -
373C HIS* 3.1 40.2 + - + -
374C GLY* 4.8 0.6 - - - -
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Residues in contact with PHE 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C LEU* 3.9 14.5 - - + +
289C LEU* 4.3 5.2 - - + -
295C ILE* 4.0 27.6 - - + -
298C MET* 3.4 28.0 - - + -
299C ARG* 3.7 21.1 - - + -
302C ALA* 3.9 11.2 - - + -
312C THR* 4.5 3.1 - - + -
314C PHE* 3.5 30.7 - + + -
327C ALA 2.9 14.7 + - - +
328C ALA* 3.5 11.4 - - - +
330C HIS* 1.3 74.5 - - - +
332C ASP* 1.3 59.0 + - - +
334C TRP* 3.1 19.2 + + - -
335C VAL* 2.8 51.7 + - + +
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Residues in contact with ASP 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C ARG* 2.8 30.3 + - - -
119C VAL* 3.6 13.5 - - + +
312C THR* 4.3 3.5 + - - -
314C PHE* 3.4 21.7 - - - -
328C ALA 2.7 25.3 + - - +
329C ILE* 3.5 7.8 - - - +
330C HIS 3.3 0.2 - - - -
331C PHE* 1.3 74.4 - - - +
333C THR* 1.3 57.6 + - - +
334C TRP 3.6 0.2 + - - -
335C VAL* 3.9 4.1 - - - +
338C PHE* 3.4 33.8 - - + +
340C ILE 5.0 0.5 - - - +
341C GLN* 2.5 37.3 + - - +
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Residues in contact with THR 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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108C TYR* 4.2 13.9 - - + -
114C LYS* 3.5 26.7 - - + -
115C SER* 2.7 32.2 + - - -
116C ARG* 3.6 21.7 + - + +
117C GLU 6.1 0.2 - - - -
119C VAL* 3.6 13.0 - - + +
329C ILE 2.6 21.1 + - - -
330C HIS 3.4 5.8 - - - -
331C PHE 3.1 0.4 - - - -
332C ASP* 1.3 77.8 - - - +
334C TRP* 1.3 52.7 + - - +
367C ALA* 3.4 22.6 + - + +
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Residues in contact with TRP 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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108C TYR* 4.1 5.6 - - + +
111C LEU* 3.2 48.0 + - + -
112C GLY* 3.8 11.2 - - - -
113C GLY 3.4 24.5 - - - +
115C SER* 2.5 26.0 + - - -
299C ARG* 3.4 42.4 - - + -
303C ASP* 4.2 12.1 - - - -
330C HIS 3.2 9.0 + - - +
331C PHE* 3.1 30.3 + + - +
333C THR* 1.3 78.8 - - - +
335C VAL* 1.3 97.8 + - + +
336C PRO* 3.3 14.6 - - + +
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Residues in contact with VAL 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C ARG* 2.7 28.8 + - - -
302C ALA* 3.9 20.0 - - + -
303C ASP* 5.3 0.9 - - - +
312C THR* 4.0 10.8 - - + +
331C PHE* 2.8 31.3 + - + +
332C ASP* 3.9 7.9 - - - +
333C THR 3.8 0.4 - - - -
334C TRP* 1.3 92.0 - - + +
336C PRO* 1.3 70.7 - - + +
337C ASN* 3.3 22.7 - - - +
338C PHE* 3.6 25.1 + - + +
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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
------------------------------------------------------------
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