Contacts of the helix formed by residues 327 - 343 (chain C) in PDB entry 1ZMC
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 LEU 327 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320C ASP* 3.9 1.1 + - - +
325C PRO* 3.0 25.9 + - + -
326C MET* 1.3 83.5 - - - +
328C ALA* 1.3 64.9 + - - +
329C HIS* 3.4 14.1 - - + +
330C LYS* 3.1 10.3 + - + +
331C ALA* 3.0 20.8 + - - +
354C VAL* 4.4 4.3 - - + -
355C PRO 3.4 25.8 - - - +
356C SER* 4.0 16.2 - - - +
357C VAL 6.1 0.9 - - - +
480C FAD 3.1 32.7 + - + +
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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
----------------------------------------------------------
16C PRO* 3.8 11.2 - - + +
45C CYS* 3.8 16.8 - - - -
50C CYS* 4.0 0.9 - - - -
327C LEU* 1.3 69.1 - - - +
329C HIS* 1.3 57.1 + - - +
331C ALA* 2.9 20.0 + - - +
332C GLU* 3.0 18.0 + - - +
480C FAD 2.8 33.7 + - + +
452D HIS* 3.5 30.5 - - + -
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Residues in contact with HIS 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327C LEU* 3.7 12.2 - - + +
328C ALA* 1.3 79.4 - - - +
330C LYS* 1.3 61.0 + - - +
332C GLU* 3.9 8.9 - - - +
333C ASP* 3.2 29.5 + - - +
354C VAL* 3.7 22.6 - - + +
355C PRO* 2.9 33.1 + - + +
356C SER* 5.2 2.5 - - - -
357C VAL* 5.6 2.5 - - + -
480C FAD 3.2 19.9 + + - -
449D CYS* 3.8 9.4 - - - -
450D HIS 3.0 28.3 - - - +
451D ALA* 3.9 9.6 - - + -
452D HIS* 3.0 31.1 + - + +
457D GLU* 5.1 1.6 - - - +
460D ARG* 5.1 3.1 - - - +
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Residues in contact with LYS 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C GLY* 3.4 21.0 + - - -
320C ASP* 5.3 0.2 - - - +
322C VAL* 3.7 2.2 + - - +
323C ALA 3.0 27.4 + - - -
324C GLY* 3.9 10.0 + - - -
325C PRO* 3.3 36.1 + - + +
326C MET* 5.5 0.4 - - - +
327C LEU* 3.1 17.2 + - + +
328C ALA 3.1 1.0 - - - -
329C HIS* 1.3 81.3 - - - +
331C ALA* 1.3 65.2 + - - +
333C ASP* 3.7 4.3 + - - +
334C GLU* 2.7 60.8 + - + +
349C ILE* 6.2 0.9 - - + -
351C TYR* 3.9 14.6 - - + -
354C VAL* 4.3 15.3 - - + -
449D CYS* 5.0 1.6 - - - -
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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
----------------------------------------------------------
16C PRO* 4.4 0.2 - - + -
17C GLY* 3.4 22.8 - - - +
318C ILE* 3.7 4.3 - - - +
319C GLY* 3.8 27.1 - - - -
320C ASP* 4.7 0.4 - - - +
327C LEU 3.0 10.4 + - - +
328C ALA 2.9 9.5 + - - +
330C LYS* 1.3 76.9 - - - +
332C GLU* 1.3 63.1 + - - +
334C GLU* 3.5 2.7 + - - +
335C GLY 3.1 17.0 + - - -
480C FAD 3.7 25.1 - - - +
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Residues in contact with GLU 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C PRO* 2.9 39.1 - - - +
17C GLY* 4.2 1.3 - - - -
19C TYR* 4.7 6.6 + - - -
20C VAL* 3.7 27.1 - - + +
328C ALA 3.0 19.3 + - - +
329C HIS* 3.9 9.1 - - - +
330C LYS 3.2 0.2 - - - -
331C ALA* 1.3 74.2 - - - +
333C ASP* 1.3 68.3 + - - +
335C GLY* 3.0 2.4 + - - -
336C ILE* 3.0 25.5 + - + +
452D HIS* 4.1 22.6 + - - -
457D GLU* 4.3 10.4 - - - +
460D ARG* 5.7 3.6 + - - +
473D ASN* 5.4 5.1 + - - -
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Residues in contact with ASP 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329C HIS 3.2 18.1 + - - +
330C LYS* 4.1 4.5 - - - +
332C GLU* 1.3 80.2 - - - +
334C GLU* 1.3 63.5 + - - +
336C ILE* 3.3 5.7 + - - +
337C ILE* 2.9 33.6 + - + +
349C ILE* 4.1 23.2 - - + +
447D ARG 4.1 7.1 - - - +
449D CYS* 3.7 22.0 - - - +
460D ARG* 2.7 40.3 + - - -
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Residues in contact with GLU 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C PHE* 3.1 29.8 - - + -
318C ILE* 4.0 8.0 - - + +
319C GLY 3.0 17.7 + - - -
322C VAL* 4.0 0.7 - - - +
323C ALA 4.2 1.6 - - - +
330C LYS* 2.7 54.2 + - + +
331C ALA 3.7 3.6 - - - +
332C GLU 3.2 0.6 - - - -
333C ASP* 1.3 75.7 - - + +
335C GLY* 1.3 57.1 + - - +
337C ILE* 3.4 10.4 - - - +
338C CYS* 2.8 34.3 + - - +
349C ILE* 5.0 5.6 - - + -
351C TYR* 2.5 31.8 + - + +
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Residues in contact with GLY 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C GLY 4.2 2.2 - - - -
21C ALA* 4.0 15.8 - - - +
145C LEU* 5.5 0.4 - - - -
318C ILE* 3.4 24.0 - - - +
331C ALA 3.1 8.2 + - - -
332C GLU 3.0 7.1 + - - -
334C GLU* 1.3 76.7 - - - +
336C ILE* 1.3 61.2 + - - +
338C CYS* 3.1 3.5 + - - +
339C VAL* 3.0 28.4 + - - +
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Residues in contact with ILE 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C VAL* 3.4 30.0 - - + +
21C ALA* 4.7 0.6 - - - +
24C LYS* 3.7 29.4 - - + +
332C GLU* 3.0 13.2 + - + +
333C ASP* 3.8 5.2 - - - +
335C GLY* 1.3 77.2 - - - +
337C ILE* 1.3 66.4 + - + +
339C VAL* 3.4 2.3 + - - +
340C GLU* 2.9 52.7 + - - +
447D ARG* 4.8 3.6 - - - +
460D ARG* 6.3 1.1 - - - +
464D LEU* 5.4 4.5 - - + -
472D ILE* 3.6 22.7 - - + -
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Residues in contact with ILE 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C PHE* 3.9 16.2 - - + -
333C ASP* 2.9 29.7 + - + +
334C GLU* 3.4 12.1 - - - +
336C ILE* 1.3 85.5 - - + +
338C CYS* 1.3 60.5 + - - +
340C GLU* 3.8 16.2 - - - +
341C GLY 3.2 14.4 + - - -
346C ALA 4.5 1.5 - - - +
347C VAL* 3.5 25.1 - - + +
348C HIS 3.7 21.1 - - - +
349C ILE* 3.7 32.3 - - + -
447D ARG* 4.4 10.3 - - + +
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Residues in contact with CYS 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C LEU* 4.0 9.0 - - + -
307C ARG 3.9 7.5 - - - +
308C PHE* 3.7 18.4 - - + -
316C TYR* 3.4 41.6 - - - -
318C ILE* 3.9 9.9 - - + -
334C GLU 2.8 19.7 + - - +
335C GLY* 3.1 4.0 + - - +
337C ILE* 1.3 76.5 - - - +
339C VAL* 1.3 65.8 + - + +
341C GLY* 3.0 3.9 + - - -
342C MET* 3.0 30.2 + - - +
347C VAL* 4.9 0.7 - - - -
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Residues in contact with VAL 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C VAL* 5.0 1.6 - - + -
21C ALA* 3.4 28.9 - - + +
24C LYS* 3.8 5.4 - - + +
25C ALA* 3.3 32.8 - - + +
28C LEU* 3.3 23.3 - - + -
30C PHE* 4.3 5.0 - - + -
145C LEU* 4.5 10.1 - - + -
335C GLY 3.0 16.9 + - - +
336C ILE 3.7 2.9 - - - +
338C CYS* 1.3 77.1 - - - +
340C GLU* 1.3 59.6 + - - +
342C MET* 3.1 29.0 + - + +
343C ALA* 3.1 12.5 + - - +
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Residues in contact with GLU 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C LYS* 4.0 16.8 + - + -
28C LEU* 3.9 20.5 - - + +
336C ILE* 2.9 39.4 + - + +
337C ILE* 3.8 12.4 - - - +
338C CYS 3.2 0.2 - - - -
339C VAL* 1.3 76.5 - - - +
341C GLY* 1.3 58.6 + - - +
343C ALA* 3.4 4.5 + - - +
344C GLY 3.4 3.3 + - - -
345C GLY* 2.8 29.0 + - - -
346C ALA 4.7 9.6 - - - +
347C VAL* 5.0 0.2 - - - -
447D ARG* 3.0 43.6 + - - -
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Residues in contact with GLY 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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307C ARG* 3.1 33.0 + - - -
316C TYR* 5.7 1.3 - - - -
337C ILE 3.2 5.9 + - - -
338C CYS 3.0 7.5 + - - -
340C GLU* 1.3 75.1 - - - +
342C MET* 1.3 57.7 + - - +
343C ALA 3.0 1.3 - - - -
344C GLY* 2.7 21.5 + - - -
345C GLY 3.7 2.5 - - - -
347C VAL* 3.5 16.6 - - - -
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Residues in contact with MET 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C VAL* 3.8 30.5 - - + -
30C PHE* 4.1 16.3 - - + -
143C ASN* 4.2 18.0 + - + +
145C LEU* 4.2 24.9 - - + -
316C TYR* 3.5 55.1 - - + +
338C CYS* 3.0 26.1 + - - +
339C VAL* 3.3 16.8 - - - +
341C GLY* 1.3 74.8 - - - +
343C ALA* 1.3 57.4 + - - +
344C GLY 3.1 3.3 + - - -
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Residues in contact with ALA 343 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C LEU* 4.1 20.4 - - + +
30C PHE* 4.0 19.3 - - + -
339C VAL 3.1 13.0 + - - +
340C GLU* 3.8 5.8 - - - +
341C GLY 3.0 1.0 - - - -
342C MET* 1.3 77.5 - - - +
344C GLY* 1.3 57.4 + - - +
345C GLY 3.5 2.7 + - - +
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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
------------------------------------------------------------
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