Contacts of the helix formed by residues 31 - 47 (chain M) in PDB entry 5I2D
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 GLY 31 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42L ARG* 2.8 27.8 + - - -
30M ARG* 1.3 75.9 - - - +
32M PHE* 1.3 61.2 + - - -
33M GLY 3.2 3.2 + - - -
34M VAL* 3.7 3.9 + - - -
35M THR* 2.8 23.1 + - - -
193M ASP* 2.7 15.7 + - - -
854N PRO* 5.7 0.4 - - - -
856N GLU* 4.4 7.4 - - - -
857N ASP* 4.8 4.9 - - - -
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Residues in contact with PHE 32 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43L ILE* 3.8 31.2 - - + -
46L SER* 4.4 6.7 - - - -
47L SER* 3.1 28.0 - - - -
217L ILE* 4.0 14.4 - - + -
218L LEU* 5.7 0.7 - - + -
221L HIS* 3.7 40.4 - + + +
28M LEU* 4.4 14.8 - - + -
29M GLU* 3.0 38.3 + - + +
30M ARG 3.2 6.5 - - - -
31M GLY* 1.3 76.5 - - - +
33M GLY* 1.3 58.6 + - - +
34M VAL 3.4 0.4 - - - -
35M THR* 3.6 16.3 - - + -
36M LEU* 2.9 36.9 + - + +
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Residues in contact with GLY 33 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28M LEU* 4.5 2.2 - - - -
31M GLY 3.2 1.8 - - - -
32M PHE* 1.3 79.2 - - - +
34M VAL* 1.3 57.5 + - - +
37M GLY* 2.9 20.6 + - - -
181M VAL* 3.5 21.0 - - - +
193M ASP* 3.2 19.8 + - - +
195M LEU* 3.4 27.3 - - - +
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Residues in contact with VAL 34 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38L ASN* 5.6 0.2 + - - -
42L ARG* 3.5 31.9 - - - +
31M GLY* 3.7 4.2 + - - +
33M GLY* 1.3 73.4 - - - +
35M THR* 1.3 62.7 + - - +
36M LEU 3.2 0.4 - - - -
37M GLY 3.6 1.6 - - - +
38M ASN* 2.9 43.0 + - - +
179M PHE* 4.1 13.9 - - + -
181M VAL* 3.9 20.6 - - + -
193M ASP* 5.5 0.7 - - - +
857N ASP* 6.0 1.1 - - - +
978N ARG* 3.5 33.9 - - + +
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Residues in contact with THR 35 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38L ASN* 5.9 0.9 - - - +
39L PRO* 3.9 32.5 - - + +
42L ARG* 2.8 34.3 + - - +
43L ILE* 4.1 18.6 - - + +
218L LEU* 4.6 6.8 - - + +
31M GLY 2.8 14.2 + - - -
32M PHE* 3.3 21.4 + - + -
33M GLY 3.3 0.6 - - - -
34M VAL* 1.3 78.9 - - - +
36M LEU* 1.3 58.7 + - + +
39M PRO* 3.1 23.6 - - - +
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Residues in contact with LEU 36 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218L LEU* 4.0 26.7 - - + -
221L HIS* 4.2 25.8 - - + +
222L LEU* 4.2 20.0 - - + -
225L PHE* 4.0 13.5 - - + -
25M LEU* 3.8 29.6 - - + -
28M LEU* 4.2 16.8 - - + -
32M PHE* 2.9 18.8 + - + +
35M THR* 1.3 79.5 - - + +
37M GLY* 1.3 64.5 + - - +
38M ASN 3.4 0.2 - - - -
39M PRO* 3.3 8.9 - - + +
40M LEU* 3.3 24.0 - - + +
195M LEU* 3.8 11.7 - - + -
218M LEU* 5.7 1.4 - - + +
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Residues in contact with GLY 37 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33M GLY 2.9 19.8 + - - -
34M VAL 3.4 0.6 + - - -
36M LEU* 1.3 79.9 - - - +
38M ASN* 1.3 60.6 + - - +
40M LEU* 3.9 2.1 - - - +
41M ARG* 3.3 22.3 + - - +
179M PHE* 3.9 26.3 - - - +
195M LEU* 4.1 9.6 - - - -
197M LEU* 4.7 6.5 - - - +
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Residues in contact with ASN 38 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38L ASN* 5.2 3.6 - - - +
34M VAL* 2.9 28.9 + - - +
37M GLY* 1.3 71.9 - - - +
39M PRO* 1.3 69.1 - - + +
41M ARG* 3.4 4.8 + - - +
42M ARG* 3.3 30.7 + - - +
179M PHE* 3.1 25.0 - - - -
978N ARG* 2.6 37.3 + - - +
979N THR* 3.4 28.7 - - - +
981N GLU* 5.4 1.7 - - - +
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Residues in contact with PRO 39 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35L THR* 4.0 25.1 - - + +
39L PRO* 3.5 24.9 - - + -
218L LEU* 6.2 0.9 - - + -
35M THR* 3.1 25.8 - - - +
36M LEU* 3.3 9.0 - - - +
38M ASN* 1.3 94.3 - - + +
40M LEU* 1.3 56.1 + - - +
42M ARG* 3.4 5.0 + - + +
43M ILE* 3.0 36.5 + - - +
218M LEU* 3.9 25.6 - - + -
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Residues in contact with LEU 40 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222L LEU* 5.1 2.7 - - + -
225L PHE* 3.8 30.7 - - + -
36M LEU* 3.3 19.7 - - + +
37M GLY* 3.9 4.3 - - - +
38M ASN 3.3 0.4 - - - -
39M PRO* 1.3 80.5 - - + +
41M ARG* 1.3 58.3 + - - +
43M ILE* 3.4 3.0 + - + +
44M LEU* 2.8 46.6 + - + +
195M LEU* 5.3 0.2 - - + -
197M LEU* 4.4 17.3 - - + -
211M LEU* 3.9 16.2 - - + -
214M ALA* 4.2 9.2 - - + +
215M VAL* 3.6 33.9 - - + +
218M LEU* 4.6 13.5 - - + -
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Residues in contact with ARG 41 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37M GLY 3.3 12.3 + - - +
38M ASN* 3.8 8.7 - - - +
39M PRO 3.3 0.4 - - - -
40M LEU* 1.3 78.0 - - - +
42M ARG* 1.3 70.5 + - + +
44M LEU* 3.9 0.5 - - - +
45M LEU* 3.2 46.8 + - + +
177M VAL* 3.4 46.3 + - + +
178M ALA* 5.3 0.6 - - - +
179M PHE* 4.3 23.1 - - + -
197M LEU* 5.7 0.4 - - + +
981N GLU* 5.1 8.3 + - - -
854O ALA* 4.4 14.8 - - - +
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Residues in contact with ARG 42 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31L GLY* 2.9 35.6 + - - -
34L VAL* 3.6 25.3 - - - +
35L THR* 2.7 31.4 + - + +
38M ASN* 3.3 21.2 + - - +
39M PRO 3.7 5.8 - - - +
41M ARG* 1.3 85.8 - - + +
43M ILE* 1.3 54.8 + - - +
45M LEU* 3.6 4.5 + - - +
46M SER* 2.6 35.6 + - - -
979N THR 5.5 3.4 - - - -
981N GLU* 3.7 30.5 + - - +
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Residues in contact with ILE 43 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32L PHE* 4.1 21.1 - - + -
35L THR* 4.2 9.4 - - + -
39M PRO 3.0 24.2 + - - +
40M LEU* 3.9 4.0 - - + +
42M ARG* 1.3 75.1 - - - +
44M LEU* 1.3 61.7 + - - +
46M SER* 3.7 5.6 - - - -
47M SER* 2.7 42.7 + - - -
48M ILE* 3.5 3.8 + - + -
214M ALA* 3.7 40.8 - - + +
217M ILE* 4.1 11.4 - - + -
218M LEU* 3.9 33.4 - - + +
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Residues in contact with LEU 44 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40M LEU* 2.8 37.8 + - + +
41M ARG 3.9 0.2 - - - +
43M ILE* 1.3 74.1 - - - +
45M LEU* 1.3 60.2 + - - +
48M ILE* 3.3 20.7 - - + +
172M SER* 3.6 4.0 + - - -
174M VAL* 3.5 21.6 - - + +
177M VAL* 3.6 28.3 - - + -
197M LEU* 4.4 6.5 - - + -
199M ILE* 3.7 24.9 - - + -
210M ALA* 3.3 46.2 - - + +
211M LEU* 3.7 8.1 - - + +
214M ALA* 3.8 9.2 - - + -
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Residues in contact with LEU 45 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41M ARG* 3.2 54.4 + - + +
42M ARG* 4.1 3.4 - - - +
44M LEU* 1.3 77.2 - - - +
46M SER* 1.3 59.2 + - - +
149M GLY* 3.8 0.5 - - - -
172M SER* 3.5 22.6 + - - -
174M VAL* 4.4 13.5 - - + +
175M ARG 4.6 0.7 - - - +
176M ARG* 4.5 6.1 - - - -
177M VAL* 3.9 29.6 - - + +
851O LEU* 3.7 24.5 - - + +
854O ALA* 4.2 17.0 - - + -
855O HIS* 3.6 20.2 - - + +
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Residues in contact with SER 46 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30L ARG* 5.8 4.0 - - - -
32L PHE* 4.6 5.3 - - - -
42M ARG* 2.6 24.9 + - - +
43M ILE* 3.7 0.7 - - - -
45M LEU* 1.3 78.6 - - - +
47M SER* 1.3 75.9 + - - +
48M ILE 3.5 1.9 + - - -
148M VAL* 3.2 9.4 - - - +
149M GLY* 2.9 28.1 + - - -
172M SER* 5.8 0.2 - - - -
855O HIS* 3.8 19.5 - - - -
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Residues in contact with SER 47 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32L PHE* 3.1 34.5 - - - -
43M ILE* 2.7 31.1 + - - -
46M SER* 1.3 77.7 + - - +
48M ILE* 1.3 61.7 + - - -
49M PRO* 3.3 10.0 - - - +
148M VAL* 3.7 12.8 - - - +
217M ILE* 3.7 17.1 - - - +
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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
------------------------------------------------------------
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