Contacts of the helix formed by residues 31 - 47 (chain L) in PDB entry 5X22
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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42K ARG* 3.1 23.7 + - - -
30L ARG* 1.3 76.0 - - - +
32L PHE* 1.3 58.8 + - - +
33L GLY 3.2 2.9 - - - -
34L VAL* 3.2 10.4 - - - +
35L THR* 2.7 23.6 + - - -
193L ASP* 3.1 13.6 + - - -
854M PRO* 5.7 1.1 - - - -
856M GLU* 4.7 6.5 - - - -
857M ASP* 5.0 2.9 - - - -
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Residues in contact with PHE 32 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43K ILE* 3.9 24.5 - - + -
46K SER* 4.8 5.2 - - - -
47K SER* 3.1 27.1 - - - -
217K ILE* 3.6 25.4 - - + -
218K LEU* 5.7 0.2 - - + -
221K HIS* 3.4 43.7 - + + +
28L LEU* 4.1 14.6 - - + -
29L GLU* 3.0 36.6 + - + +
30L ARG 3.4 6.0 - - - -
31L GLY* 1.3 75.3 - - - +
33L GLY* 1.3 60.3 + - - +
34L VAL 3.4 0.2 - - - -
35L THR* 3.7 15.7 - - + -
36L LEU* 2.9 36.1 + - + +
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Residues in contact with GLY 33 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28L LEU* 4.1 11.2 - - - +
32L PHE* 1.3 78.5 - - - +
34L VAL* 1.3 57.0 + - - +
37L GLY* 2.9 21.0 + - - -
181L VAL* 3.5 15.7 - - - +
193L ASP* 3.2 27.5 + - - +
195L LEU* 3.4 18.3 - - - +
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Residues in contact with VAL 34 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42K ARG* 3.3 16.8 - - - +
31L GLY* 3.2 21.5 - - - +
33L GLY* 1.3 71.5 - - - +
35L THR* 1.3 64.6 + - - +
36L LEU 3.2 0.2 - - - -
37L GLY 4.2 0.2 - - - +
38L ASN* 2.9 49.4 + - - +
179L PHE* 4.2 8.5 - - + -
181L VAL* 3.6 15.0 - - + +
193L ASP* 4.9 2.2 - - - +
857M ASP* 5.0 3.4 - - - +
978M ARG* 3.3 34.5 - - + +
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Residues in contact with THR 35 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38K ASN* 6.0 0.2 - - - +
39K PRO* 3.9 21.6 - - + +
42K ARG* 2.8 27.3 + - + +
43K ILE* 3.8 34.5 - - + +
218K LEU* 4.7 5.0 - - + +
31L GLY 2.7 22.4 + - - -
32L PHE* 3.7 19.0 - - + -
34L VAL* 1.3 79.1 - - - +
36L LEU* 1.3 57.8 + - - +
39L PRO* 3.1 24.5 - - - +
978M ARG 5.7 0.2 - - - -
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Residues in contact with LEU 36 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218K LEU* 3.7 28.3 - - + -
221K HIS* 3.9 44.2 - - + +
222K LEU* 4.2 16.4 - - + -
225K PHE* 4.2 8.3 - - + -
25L LEU* 3.9 26.5 - - + -
28L LEU* 4.2 5.8 - - + -
32L PHE* 2.9 22.1 + - + +
35L THR* 1.3 76.0 - - - +
37L GLY* 1.3 64.8 + - - +
39L PRO* 3.2 7.8 - - - +
40L LEU* 3.2 26.3 - - + +
195L LEU* 4.1 11.7 - - + -
218L LEU* 5.6 1.7 - - + +
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Residues in contact with GLY 37 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33L GLY 2.9 20.6 + - - -
34L VAL 3.2 0.8 + - - -
36L LEU* 1.3 78.8 - - - +
38L ASN* 1.3 63.0 + - - +
40L LEU* 3.5 3.8 + - - +
41L ARG* 3.2 21.5 + - - +
179L PHE* 3.9 22.9 - - - -
195L LEU* 4.0 10.2 - - - +
197L LEU* 4.6 6.8 - - - +
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Residues in contact with ASN 38 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38K ASN* 5.6 1.6 - - - +
34L VAL* 2.9 27.9 + - - +
37L GLY* 1.3 70.9 - - - +
39L PRO* 1.3 68.4 - - + +
41L ARG* 3.2 9.6 + - - +
42L ARG* 3.0 32.5 + - - +
179L PHE* 3.3 23.7 - - - -
978M ARG* 3.2 25.6 + - - +
979M THR* 3.3 34.4 - - - +
981M GLU* 4.5 5.4 - - - +
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Residues in contact with PRO 39 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35K THR* 3.8 26.0 - - + +
39K PRO* 3.4 24.0 - - + -
218K LEU* 5.9 0.4 - - + -
35L THR 3.1 27.4 - - - +
36L LEU* 3.2 9.0 - - - +
38L ASN* 1.3 93.6 - - + +
40L LEU* 1.3 55.3 + - - +
42L ARG* 3.2 6.1 + - + +
43L ILE* 2.8 37.2 + - - +
218L LEU* 3.9 22.9 - - + -
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Residues in contact with LEU 40 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222K LEU* 4.6 2.9 - - + -
225K PHE* 3.7 34.3 - - + -
36L LEU* 3.2 21.3 - - + +
37L GLY* 3.5 5.6 + - - +
38L ASN 3.3 0.4 - - - -
39L PRO* 1.3 76.0 - - - +
41L ARG* 1.3 58.0 + - - +
43L ILE* 3.8 3.9 - - + +
44L LEU* 2.8 47.3 + - + +
195L LEU* 5.3 0.9 - - + -
197L LEU* 4.8 10.3 - - + -
211L LEU* 4.2 10.5 - - + -
214L ALA* 4.5 6.1 - - + +
215L VAL* 3.7 35.4 - - + +
218L LEU* 4.0 22.2 - - + -
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Residues in contact with ARG 41 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37L GLY 3.2 12.0 + - - +
38L ASN* 3.2 14.6 + - - +
40L LEU* 1.3 76.7 - - - +
42L ARG* 1.3 71.6 + - + +
44L LEU* 3.3 2.0 + - - +
45L LEU* 3.1 47.6 + - + +
177L VAL* 3.6 45.6 + - + -
178L ALA* 5.4 0.8 - - - +
179L PHE* 4.1 25.8 - - + -
197L LEU* 5.6 1.5 - - + +
981M GLU* 5.0 9.7 + - - -
854N ALA* 4.6 12.3 - - - +
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Residues in contact with ARG 42 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31K GLY* 3.0 31.1 + - - -
34K VAL* 3.5 24.3 - - - +
35K THR* 2.9 37.5 + - - +
38L ASN* 3.0 27.1 + - - +
39L PRO* 3.6 4.0 - - - +
41L ARG* 1.3 85.1 - - + +
43L ILE* 1.3 56.4 + - - +
45L LEU* 3.6 4.1 + - - +
46L SER* 2.5 36.1 + - - +
979M THR 5.3 2.5 - - - -
981M GLU* 3.4 41.4 + - - +
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Residues in contact with ILE 43 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32K PHE* 4.1 12.6 - - + -
35K THR* 3.9 21.3 - - + +
39L PRO 2.8 22.6 + - - +
40L LEU* 3.8 4.7 - - - +
42L ARG* 1.3 74.9 - - - +
44L LEU* 1.3 62.2 + - - +
46L SER* 3.8 4.0 - - - -
47L SER* 2.7 34.6 + - - +
48L ILE* 3.8 2.9 + - + -
214L ALA* 3.6 33.2 - - + +
217L ILE* 4.0 22.9 - - + -
218L LEU* 3.6 38.6 - - + +
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Residues in contact with LEU 44 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40L LEU* 2.8 31.6 + - + +
41L ARG 3.3 1.1 + - - +
43L ILE* 1.3 73.8 - - - +
45L LEU* 1.3 62.7 + - - +
48L ILE* 3.6 15.5 - - + +
172L SER* 3.7 2.3 + - - -
174L VAL* 3.4 27.0 - - + +
177L VAL* 3.7 24.9 - - + -
197L LEU* 4.2 12.8 - - + -
199L ILE* 3.6 27.6 - - + -
210L ALA* 3.4 45.8 - - + +
211L LEU* 3.8 8.5 - - + +
214L ALA* 3.8 8.7 - - + -
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Residues in contact with LEU 45 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41L ARG* 3.1 52.7 + - + +
42L ARG* 4.1 4.3 - - - +
44L LEU* 1.3 78.3 - - - +
46L SER* 1.3 62.4 + - - +
48L ILE 5.2 0.4 + - - -
149L GLY* 3.9 1.4 - - - -
172L SER* 3.6 23.5 + - - -
174L VAL* 4.1 14.4 - - + +
175L ARG 5.1 0.7 - - - +
176L ARG* 4.6 3.4 - - - -
177L VAL* 3.9 30.1 - - + +
851N LEU* 4.1 21.6 - - + +
854N ALA* 4.2 17.7 - - + -
855N HIS* 3.7 14.1 + - + +
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Residues in contact with SER 46 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30K ARG* 5.1 12.1 + - - -
32K PHE* 4.8 4.4 - - - -
42L ARG* 2.5 27.5 + - - +
43L ILE* 3.8 0.9 - - - -
45L LEU* 1.3 80.1 - - - +
47L SER* 1.3 69.1 + - - +
48L ILE 3.7 1.1 - - - -
148L VAL* 3.3 8.0 - - - +
149L GLY* 3.0 25.3 + - - -
855N HIS* 3.7 21.3 - - - -
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Residues in contact with SER 47 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29K GLU* 5.7 0.2 - - - +
32K PHE* 3.0 31.7 - - - -
43L ILE* 2.7 24.0 + - - -
46L SER* 1.3 78.7 + - - +
48L ILE* 1.3 60.9 + - - +
49L PRO* 3.3 9.5 - - - +
148L VAL* 3.4 14.8 - - - +
217L ILE* 3.7 27.8 - - - +
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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