Contacts of the helix formed by residues 336 - 356 (chain C) in PDB entry 1ML3
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 GLU 336 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B VAL* 4.8 8.1 - - - +
12C ARG* 2.7 37.1 + - + +
13C ILE* 4.0 11.3 - - + +
16C MET* 4.4 11.2 - - + -
55C VAL* 3.6 5.4 - - - +
56C HIS* 2.6 33.7 + - - +
253C PRO 4.5 7.5 - - - +
254C ASP* 3.0 20.3 - - - +
334C ASP* 3.1 4.3 + - - +
335C ASN* 1.3 87.2 + - - +
337C TRP* 1.3 57.7 + - - +
340C SER* 2.8 33.3 + - - -
1360C NAD 4.1 17.1 + - - +
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Residues in contact with TRP 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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16C MET* 3.2 40.4 - - + -
19C GLN* 3.1 41.3 - - + -
20C ALA 5.1 0.2 - - - -
23C GLU* 2.9 32.7 + - - -
56C HIS* 3.7 17.5 - + + -
303C ASN* 3.4 46.5 + - + -
304C ASP 3.7 11.2 - - - -
305C ASN* 3.8 5.7 - - - +
334C ASP* 2.9 31.9 + - + +
336C GLU* 1.3 72.3 - - - +
338C GLY* 1.3 65.6 + - - +
340C SER* 3.4 3.1 + - - -
341C HIS* 3.2 45.3 + + - -
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Residues in contact with GLY 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304C ASP 4.0 6.1 + - - -
305C ASN 4.2 6.5 - - - -
306C ARG 3.8 22.2 - - - -
307C SER* 5.0 3.8 - - - -
333C TYR* 6.4 0.7 - - - -
334C ASP 2.9 18.5 + - - -
337C TRP* 1.3 71.5 - - - +
339C TYR* 1.3 64.6 + - - +
341C HIS* 3.1 6.2 + - - +
342C ARG* 3.1 28.1 + - - +
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Residues in contact with TYR 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C ILE* 4.5 8.5 - - + -
134C SER* 2.7 48.1 - - - -
135C ALA 2.8 4.5 + - - -
163C ASN* 3.4 28.2 - - - +
164C ALA 2.9 20.3 + - - -
165C SER* 3.5 25.8 - - - -
166C CYS* 3.6 8.7 - - - +
169C ASN* 3.6 11.6 - - - +
334C ASP 4.3 0.6 + - - -
335C ASN* 3.6 20.8 + - - +
336C GLU 4.1 1.1 + - - +
337C TRP 3.5 0.2 - - - -
338C GLY* 1.3 73.7 - - - +
340C SER* 1.3 63.9 + - - +
342C ARG* 3.1 9.5 + - - +
343C VAL* 2.9 44.6 + - + +
1360C NAD 3.6 17.9 - + + -
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Residues in contact with SER 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C ILE* 4.0 9.0 + - - +
16C MET* 3.0 43.0 - - - +
17C VAL* 3.6 13.4 + - - +
20C ALA* 4.1 3.8 - - - +
336C GLU 2.8 21.7 + - - -
337C TRP* 3.5 7.9 - - - -
339C TYR* 1.3 79.7 - - - +
341C HIS* 1.3 63.0 + - - +
343C VAL* 3.2 17.7 + - - +
344C VAL* 3.4 12.3 + - - +
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Residues in contact with HIS 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C ALA* 3.2 28.0 - - + +
23C GLU* 2.6 33.3 + - - -
24C ASP* 3.8 27.8 + - - +
305C ASN* 3.1 34.3 + - + +
337C TRP* 3.2 26.7 + + - +
338C GLY 3.1 6.9 + - - +
340C SER* 1.3 77.2 - - - +
342C ARG* 1.3 77.4 + - - +
344C VAL* 3.2 6.3 + - - +
345C ASP* 2.8 35.4 + - - +
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Residues in contact with ARG 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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146C MET* 3.9 14.4 - - + +
163C ASN* 3.8 15.5 - - - +
169C ASN* 3.9 14.1 - - - +
287C GLY 3.5 17.4 + - - -
288C ILE* 3.7 19.9 - - - +
305C ASN* 2.6 33.9 + - - +
306C ARG 3.6 0.2 - - - -
307C SER* 2.9 43.2 + - - +
338C GLY 3.1 15.8 + - - +
339C TYR* 3.1 11.0 + - - +
341C HIS* 1.3 88.0 + - - +
343C VAL* 1.3 58.0 + - - +
345C ASP* 2.8 33.1 + - - +
346C LEU* 2.8 32.2 + - - +
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Residues in contact with VAL 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C VAL* 4.0 14.6 - - + -
108C ILE* 4.0 35.2 - - + -
132C VAL* 4.7 11.2 - - + -
134C SER* 4.7 6.3 - - - -
163C ASN* 3.7 14.1 - - + +
339C TYR* 2.9 50.6 + - + +
340C SER* 3.2 11.2 + - - +
342C ARG* 1.3 76.1 - - - +
344C VAL* 1.3 56.0 + - - +
346C LEU* 3.6 2.4 - - - +
347C VAL* 3.0 35.3 + - + +
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Residues in contact with VAL 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C VAL* 3.9 32.1 - - + +
20C ALA* 4.3 2.7 - - + -
21C LEU* 4.1 19.3 - - + +
24C ASP* 4.8 7.4 - - - +
26C LEU* 3.7 29.8 - - + -
31C ILE* 3.8 13.7 - - + -
108C ILE* 6.1 0.7 - - + -
340C SER 3.8 11.4 - - - +
341C HIS* 3.2 9.0 + - - +
343C VAL* 1.3 73.6 - - - +
345C ASP* 1.3 68.0 + - - +
346C LEU 3.0 1.7 + - - -
347C VAL* 3.2 6.5 + - - +
348C ARG* 2.9 26.5 + - + +
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Residues in contact with ASP 345 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C ASP* 5.6 2.9 - - - +
146C MET* 3.6 27.3 - - + +
288C ILE* 5.8 1.8 - - - -
341C HIS* 2.8 23.3 + - - +
342C ARG* 2.8 37.8 + - - +
344C VAL* 1.3 79.1 - - - +
346C LEU* 1.3 60.9 + - - +
348C ARG* 3.7 24.5 + - - +
349C HIS* 3.2 15.1 + - - +
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Residues in contact with LEU 346 (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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132C VAL* 4.2 16.6 - - + -
144C LEU* 3.9 34.3 - - + -
146C MET* 3.6 22.0 - - - -
150C HIS* 4.4 4.9 - - + -
161C VAL* 4.6 4.0 - - + -
162C SER 4.4 6.1 - - - +
163C ASN* 3.1 37.2 - - + +
342C ARG 2.8 16.9 + - - +
343C VAL 3.6 4.5 - - - +
345C ASP* 1.3 74.3 - - - +
347C VAL* 1.3 59.4 + - - +
348C ARG 2.9 1.6 - - - -
349C HIS* 2.6 29.2 + - + +
350C MET* 2.8 22.8 + - + +
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Residues in contact with VAL 347 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C VAL* 4.4 13.2 - - + -
31C ILE* 5.5 5.4 - - + -
106C TYR* 3.9 32.5 - - + -
108C ILE* 3.2 31.2 - - + -
132C VAL* 4.1 18.4 - - + -
343C VAL* 3.0 18.7 + - + +
344C VAL* 3.7 7.6 - - + +
346C LEU* 1.3 79.0 - - - +
348C ARG* 1.3 62.5 + - + +
350C MET* 3.5 13.3 + - - +
351C ALA* 3.5 18.4 + - - +
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Residues in contact with ARG 348 (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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3C ILE* 6.5 0.7 - - + -
24C ASP* 6.1 1.3 - - - +
26C LEU* 3.4 40.2 - - - +
30C GLU* 3.4 31.6 + - - -
31C ILE* 4.0 20.9 - - + -
344C VAL* 2.9 21.0 + - - +
345C ASP* 3.8 24.3 + - - +
347C VAL* 1.3 77.2 - - + +
349C HIS* 1.3 63.9 + - - +
351C ALA* 3.2 8.2 + - - +
352C SER* 3.1 22.3 + - - -
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Residues in contact with HIS 349 (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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146C MET* 4.4 6.9 - - + +
150C HIS* 3.1 54.5 + + + -
151C HIS* 3.9 10.1 - + - -
153C TYR* 4.3 13.8 - + + +
345C ASP 3.2 14.0 + - - +
346C LEU* 2.6 23.1 + - + +
348C ARG* 1.3 67.8 - - - +
350C MET* 1.3 59.1 + - + +
351C ALA 2.8 11.6 + - - -
352C SER* 3.1 23.8 + - - -
353C LYS* 3.2 50.4 + - + +
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Residues in contact with MET 350 (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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106C TYR* 2.8 17.9 + - + +
130C LYS* 4.3 22.2 - - + -
131C VAL 4.9 2.0 - - - +
132C VAL* 3.7 19.1 - - + -
144C LEU* 5.0 0.2 - - + -
153C TYR* 3.3 58.2 + - + +
158C HIS 4.8 0.7 - - - +
159C HIS 5.6 0.7 - - - +
161C VAL* 3.6 32.8 - - + -
346C LEU* 2.8 32.6 + - + +
347C VAL* 3.8 9.2 - - - +
348C ARG 3.3 0.2 - - - -
349C HIS* 1.3 75.0 - - + +
351C ALA* 1.3 53.8 + - - +
354C ASP* 2.6 24.5 - - - +
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Residues in contact with ALA 351 (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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3C ILE* 4.7 15.9 - - + -
106C TYR* 3.2 30.3 - - + +
347C VAL 3.5 4.9 + - - +
348C ARG* 3.5 11.7 - - - +
349C HIS 2.8 0.4 - - - -
350C MET* 1.3 79.5 - - - +
352C SER* 1.3 64.5 + - - +
353C LYS 3.1 1.8 - - - -
354C ASP 3.2 2.1 + - - -
355C ARG* 3.1 37.9 + - + +
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Residues in contact with SER 352 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348C ARG 3.1 10.6 + - - -
349C HIS* 3.1 22.7 + - - -
351C ALA* 1.3 75.7 - - - +
353C LYS* 1.3 67.9 + - - +
354C ASP 3.1 1.8 + - - -
355C ARG* 4.4 2.2 - - - +
356C SER* 3.2 32.6 - - - -
357C ALA* 5.1 0.2 - - - +
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Residues in contact with LYS 353 (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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151C HIS* 3.0 44.4 + - - +
153C TYR* 4.3 15.6 + - + +
155C PRO* 3.0 23.0 - - + +
349C HIS* 3.2 39.2 + - + +
351C ALA 3.1 1.0 - - - -
352C SER* 1.3 82.6 - - - +
354C ASP* 1.3 67.9 + - - +
357C ALA* 3.7 20.5 - - + +
358C ARG* 5.4 0.2 - - - -
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Residues in contact with ASP 354 (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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106C TYR* 3.8 5.7 + - - -
129C ARG* 5.2 7.2 + - - +
130C LYS* 4.6 9.7 - - - -
153C TYR* 3.8 14.9 + - - -
155C PRO* 4.1 11.1 - - - +
350C MET 2.6 28.4 - - - +
351C ALA 3.4 0.9 - - - +
352C SER 3.1 1.2 + - - -
353C LYS* 1.3 96.9 - - - +
355C ARG* 1.3 85.5 + - - +
356C SER 3.2 1.3 - - - +
357C ALA* 3.8 2.5 - - - +
358C ARG* 3.0 32.2 + - - +
359C LEU* 3.4 10.4 + - + +
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Residues in contact with ARG 355 (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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3C ILE* 4.3 12.6 - - + +
105C GLU* 2.9 35.6 + - - -
106C TYR* 3.0 28.9 + - - -
129C ARG* 4.8 6.9 - - - +
351C ALA* 3.1 19.5 + - + +
352C SER* 5.4 1.3 - - - +
354C ASP* 1.3 96.6 + - - +
356C SER* 1.3 61.2 + - - +
359C LEU* 3.1 54.1 - - + +
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Residues in contact with SER 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352C SER* 3.2 21.7 + - - -
354C ASP 3.2 0.2 - - - -
355C ARG* 1.3 81.6 + - - +
357C ALA* 1.3 59.9 + - - +
358C ARG 3.7 0.4 - - - -
359C LEU 4.4 5.7 - - - +
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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