Contacts of the helix formed by residues 295 - 307 (chain C) in PDB entry 1UMD
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 ASP 295 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C ARG* 2.9 45.2 + - - -
270C TYR* 2.9 17.2 + - + +
292C ARG* 3.6 21.5 + - - +
293C LYS 3.4 1.8 + - - +
294C LYS* 1.3 77.1 - - - +
296C PRO* 1.3 72.8 - - - +
297C ILE* 3.0 9.4 + - - +
298C PRO* 3.2 31.4 - - + +
299C ARG* 3.3 12.6 + - - +
302C ARG* 5.4 0.5 + - - -
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Residues in contact with PRO 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C MET* 4.3 4.7 - - - +
49C ARG* 4.2 4.0 - - - +
72C GLY 4.4 7.0 - - - +
74C GLU* 4.2 15.5 - - + +
75C ALA* 3.5 33.7 - - + +
238C MET* 3.2 50.6 - - + +
240C VAL 5.5 0.2 - - - +
270C TYR* 4.3 1.3 - - + +
294C LYS 3.1 1.5 - - - +
295C ASP* 1.3 89.7 - - - +
297C ILE* 1.3 58.7 + - + +
299C ARG* 3.7 2.9 - - + +
300C PHE* 3.0 30.7 + - - +
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Residues in contact with ILE 297 (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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42C TYR* 3.4 29.3 - - + +
45C MET* 3.7 33.2 - - + +
46C LEU* 3.9 19.5 - - + -
49C ARG* 3.5 50.7 - - + +
74C GLU* 4.8 2.2 - - + -
295C ASP* 3.0 9.2 + - - +
296C PRO* 1.3 75.0 - - + +
298C PRO* 1.3 77.7 - - + +
300C PHE 3.3 1.0 + - - -
301C ARG* 2.9 25.8 + - - +
319C ARG* 5.0 5.6 - - - +
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Residues in contact with PRO 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C ASP* 3.2 37.5 - - + +
297C ILE* 1.3 93.2 - - + +
299C ARG* 1.3 60.4 + - - +
301C ARG* 3.3 34.4 + - + +
302C ARG* 3.0 44.9 + - - +
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Residues in contact with ARG 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C ARG* 4.1 12.3 - - - +
19C ILE* 2.9 46.7 + - + +
20C GLY 4.7 6.1 + - - +
21C GLU* 5.9 1.7 - - - +
23C GLY* 5.1 0.7 - - - -
236C ASP* 2.6 38.2 + - - -
238C MET* 3.9 22.1 + - - +
239C ASP* 3.3 20.8 + - - +
294C LYS* 4.9 10.7 + - - +
295C ASP 3.3 15.5 + - - +
296C PRO 3.7 5.8 - - - +
297C ILE 3.1 0.4 - - - -
298C PRO* 1.3 81.7 - - - +
300C PHE* 1.3 60.0 + - - +
302C ARG* 3.4 27.2 + - - +
303C PHE* 3.4 15.9 + - - +
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Residues in contact with PHE 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C ILE* 3.6 14.4 - - + -
38C LEU* 3.1 41.3 - - + -
41C LEU* 3.9 9.2 - - + -
42C TYR* 3.7 25.8 - + + -
45C MET* 3.4 24.5 - - + -
240C VAL* 3.5 24.7 - - + +
241C LEU* 4.0 12.6 - - + -
296C PRO 3.0 18.0 + - - +
297C ILE 4.1 1.6 - - - +
299C ARG* 1.3 73.0 - - - +
301C ARG* 1.3 66.9 + - - +
302C ARG 3.2 0.7 - - - -
303C PHE* 3.0 26.8 + + + +
304C LEU* 2.9 34.8 + - + +
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Residues in contact with ARG 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C TYR* 3.3 29.3 + - + -
297C ILE* 2.9 18.4 + - - +
298C PRO* 3.4 38.8 + - - +
300C PHE* 1.3 77.6 - - - +
302C ARG* 1.3 65.5 + - - +
304C LEU* 3.3 6.5 + - - +
305C GLU* 2.9 32.7 + - - +
310C TRP* 3.2 51.0 - - + +
315C GLU* 3.8 5.8 + - - -
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Residues in contact with ARG 302 (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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21C GLU* 3.7 22.8 + - - +
22C GLU* 4.7 5.7 - - - +
23C GLY* 4.2 11.2 - - - +
293C LYS 5.1 8.3 + - - -
295C ASP 5.4 0.4 + - - -
298C PRO* 3.0 35.4 + - - +
299C ARG* 3.4 34.2 + - - +
300C PHE 3.2 0.2 - - - -
301C ARG* 1.3 83.0 - - - +
303C PHE* 1.3 65.2 + - - +
305C GLU* 3.8 13.7 - - - +
306C ALA* 3.2 24.4 + - - +
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Residues in contact with PHE 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C ILE* 4.0 19.7 - - + -
23C GLY* 3.1 32.8 - - - +
24C GLU 4.2 0.9 - - - -
25C TRP* 4.1 23.3 - + + -
31C LEU* 3.7 18.2 - - + -
38C LEU* 4.3 9.9 - - + -
241C LEU* 3.6 26.5 - - + -
299C ARG 3.4 7.5 + - - +
300C PHE* 3.0 36.2 + + + +
302C ARG* 1.3 81.1 - - - +
304C LEU* 1.3 67.3 + - + +
306C ALA* 3.5 7.6 + - - +
307C ARG* 3.3 45.7 + - - +
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Residues in contact with LEU 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C LEU* 3.8 31.9 - - + +
39C ARG* 4.6 2.5 - - - +
42C TYR* 3.5 43.7 - - + -
300C PHE* 2.9 31.2 + - + +
301C ARG* 3.7 6.7 - - - +
303C PHE* 1.3 79.0 - - + +
305C GLU* 1.3 60.6 + - - +
307C ARG* 2.8 21.3 + - - +
309C LEU* 2.9 40.3 + - + +
310C TRP* 3.7 11.9 - - + -
314C TRP* 4.2 11.7 - - + -
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Residues in contact with GLU 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C ARG* 2.9 23.3 + - - +
302C ARG* 3.8 15.3 - - - +
303C PHE 3.4 0.2 - - - -
304C LEU* 1.3 77.4 - - - +
306C ALA* 1.3 61.9 + - - +
307C ARG 3.1 0.9 + - - -
308C GLY* 3.2 12.0 + - - -
310C TRP* 3.4 49.0 - - + +
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Residues in contact with ALA 306 (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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22C GLU 4.8 8.3 - - - +
23C GLY 4.4 11.2 - - - +
302C ARG 3.2 17.7 + - - +
303C PHE 3.8 5.8 - - - +
304C LEU 3.2 0.4 - - - -
305C GLU* 1.3 77.1 - - - +
307C ARG* 1.3 62.1 + - + +
308C GLY 3.5 0.6 + - - -
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Residues in contact with ARG 307 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C GLY 4.9 2.6 + - - -
24C GLU* 5.9 0.2 - - - +
25C TRP* 3.3 35.6 - - - +
31C LEU* 3.8 18.7 - - - +
38C LEU* 4.9 2.4 - - - +
303C PHE* 3.3 45.6 + - - +
304C LEU 2.8 7.6 + - - +
306C ALA* 1.3 83.8 - - + +
308C GLY* 1.3 60.9 + - - +
309C LEU* 3.2 24.2 + - + +
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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