Contacts of the helix formed by residues 48 - 62 (chain P) in PDB entry 5A31
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 48 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1M MET 4.6 12.3 - - - +
43P THR* 3.0 8.9 + - - +
44P ARG* 5.5 0.4 - - - -
46P ARG* 3.9 10.8 - - + -
47P GLY* 1.3 78.0 - - - +
49P LEU* 1.3 62.3 + - - +
50P HIS 3.4 2.0 - - - -
51P SER* 3.5 12.3 + - - +
52P SER* 3.0 26.8 + - - -
116P PHE* 3.6 36.8 - - + -
120P TYR* 3.6 24.7 - - + +
170P PHE* 4.1 16.2 - - + -
173P TYR* 4.3 12.1 - - + -
202P HIS* 3.7 29.4 - - + +
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Residues in contact with LEU 49 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C ALA* 5.2 1.0 - - - +
95C ASP* 3.1 60.1 - - + +
96C VAL* 4.0 16.9 - - + +
1M MET 4.8 2.2 - - - +
44P ARG* 6.0 2.7 - - + +
47P GLY* 3.0 32.9 + - - +
48P LEU* 1.3 74.2 - - - +
50P HIS* 1.3 67.3 + - + +
52P SER* 3.1 7.5 + - - -
53P LYS* 2.8 30.0 + - - +
94P PHE* 5.1 8.1 - - + -
95P ASP* 6.2 0.4 - - - +
120P TYR* 5.7 1.3 + - - +
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Residues in contact with HIS 50 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C VAL* 3.9 28.0 + - + +
1M MET* 3.9 37.9 - - + +
4M GLU* 3.3 48.4 + - + +
48P LEU 3.4 0.2 - - - -
49P LEU* 1.3 85.5 - - + +
51P SER* 1.3 64.4 + - - +
53P LYS* 3.5 20.8 + - - +
54P TRP* 3.1 22.3 + - - +
203P TRP* 6.4 0.2 - - - -
330P ARG* 5.5 4.9 - - - -
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Residues in contact with SER 51 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1M MET* 5.0 5.3 - - - +
43P THR* 3.2 19.1 - - - +
48P LEU* 3.5 7.5 + - - -
49P LEU 3.4 0.4 - - - -
50P HIS* 1.3 78.0 - - - +
52P SER* 1.3 58.8 + - - +
54P TRP* 3.4 7.7 + - - +
55P SER* 3.0 31.1 + - - -
202P HIS* 3.2 39.0 + - - -
203P TRP* 4.5 6.5 + - - +
204P GLY* 3.8 17.3 - - - +
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Residues in contact with SER 52 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C ALA* 4.4 9.0 - - - -
40P ALA* 4.1 9.5 - - - +
43P THR* 2.4 30.1 + - - -
44P ARG* 3.1 27.6 + - - -
48P LEU 3.0 10.0 + - - -
49P LEU* 3.1 11.9 + - - -
51P SER* 1.3 73.7 + - - +
53P LYS* 1.3 66.3 + - - +
55P SER* 3.1 7.4 + - - -
56P ALA* 2.9 25.6 + - - +
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Residues in contact with LYS 53 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C ALA* 3.9 14.5 - - + +
93C TYR* 3.3 51.0 + - + +
96C VAL* 3.6 28.9 - - + -
98C GLU* 5.0 1.5 + - - +
101C ARG* 4.8 2.2 - - - +
49P LEU 2.8 16.4 + - - +
50P HIS* 3.6 22.9 + - - +
52P SER* 1.3 76.7 - - - +
54P TRP* 1.3 63.7 + - - +
56P ALA* 3.1 2.9 + - - +
57P GLU* 3.0 31.6 + - + +
298P GLU* 4.2 22.8 + - - +
330P ARG* 5.5 6.1 - - - +
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Residues in contact with TRP 54 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36P LEU* 4.4 5.8 - - + -
50P HIS 3.1 14.5 + - - +
51P SER 3.8 2.7 - - - +
52P SER 3.3 0.2 - - - -
53P LYS* 1.3 81.2 - - - +
55P SER* 1.3 77.8 + - - +
57P GLU* 3.5 17.5 + - + +
58P LEU* 3.4 42.9 + - + +
201P LEU 4.7 2.9 - - - -
203P TRP* 3.4 62.7 - + + +
229P MET* 3.7 28.7 - - + -
232P PHE* 4.2 16.4 - + - -
264P TYR* 3.7 39.3 - + + -
298P GLU* 6.1 0.7 - - - -
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Residues in contact with SER 55 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36P LEU* 3.6 23.0 - - - +
39P ILE* 3.9 22.2 + - - +
40P ALA* 3.3 23.1 - - - +
43P THR* 4.7 0.2 + - - -
51P SER 3.0 15.1 + - - -
52P SER* 3.1 12.8 + - - -
54P TRP* 1.3 92.3 - - - +
56P ALA* 1.3 61.6 + - - +
57P GLU 3.4 0.2 + - - -
58P LEU* 3.4 2.1 + - - +
59P ALA* 3.2 17.3 + - - +
201P LEU 4.8 1.6 - - - -
203P TRP 6.2 0.2 - - - -
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Residues in contact with ALA 56 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C ASP 5.3 0.5 - - - +
88C THR* 4.3 10.4 + - - +
89C LEU* 3.7 31.1 - - - +
92C ALA* 4.6 2.5 - - + -
37P LEU* 6.3 0.4 - - - -
40P ALA* 4.7 11.4 - - + -
52P SER 2.9 18.5 + - - +
53P LYS* 3.6 5.4 - - - +
55P SER* 1.3 79.3 + - - +
57P GLU* 1.3 58.2 + - - +
59P ALA* 3.3 7.5 + - - +
60P PHE* 3.0 29.3 + - - +
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Residues in contact with GLU 57 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C LEU* 3.0 28.4 - - - +
93C TYR* 2.7 37.1 + - + +
105C PHE* 4.8 5.0 - - - -
53P LYS* 3.0 28.7 + - + +
54P TRP* 3.5 13.2 - - + +
55P SER 3.2 0.2 - - - -
56P ALA* 1.3 72.8 - - - +
58P LEU* 1.3 73.2 + - + +
60P PHE* 3.3 6.2 + - - +
61P SER* 3.0 22.3 + - - -
262P SER* 5.0 4.0 + - - +
263P SER* 5.2 11.1 - - - +
264P TYR* 5.0 14.8 - - + +
293P ASP* 5.3 0.7 - - - +
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Residues in contact with LEU 58 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36P LEU* 3.4 20.6 - - + -
54P TRP* 3.4 43.9 + - + +
55P SER 3.4 3.7 + - - +
56P ALA 3.4 0.2 - - - -
57P GLU* 1.3 79.5 - - - +
59P ALA* 1.3 64.1 + - - +
61P SER* 3.1 8.5 + - - -
62P LEU* 3.1 24.0 + - - +
228P TRP* 4.6 3.1 - - + -
232P PHE* 3.5 32.3 - - + -
259P PHE* 3.6 22.2 - - + -
262P SER* 3.8 20.6 - - - +
264P TYR* 4.4 15.9 - - + -
265P ILE* 5.4 0.7 - - + -
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Residues in contact with ALA 59 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C ASP* 5.0 2.9 - - + +
88C THR* 5.7 2.2 - - - +
33P LYS* 3.6 25.1 - - + +
36P LEU* 3.5 15.0 - - + +
37P LEU* 4.3 26.9 - - + +
55P SER 3.2 11.7 + - - +
56P ALA* 3.5 11.9 - - - +
57P GLU 3.3 0.2 - - - -
58P LEU* 1.3 77.4 - - - +
60P PHE* 1.3 63.0 + - - +
62P LEU* 3.1 22.6 + - - +
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Residues in contact with PHE 60 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C ASP* 3.8 30.1 + - + +
86C ALA* 4.2 18.8 - - + -
89C LEU* 3.3 32.1 - - + -
105C PHE* 4.2 27.4 - + + -
56P ALA 3.0 12.3 + - - +
57P GLU* 3.7 4.7 - - - +
58P LEU 3.3 0.2 - - - -
59P ALA* 1.3 72.7 - - - +
61P SER* 1.3 69.9 + - - +
62P LEU 3.3 7.3 - - - +
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Residues in contact with SER 61 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57P GLU 3.0 9.9 + - - -
58P LEU* 3.1 11.6 + - - -
60P PHE* 1.3 80.4 - - - +
62P LEU* 1.3 63.2 + - - +
258P GLY 4.0 0.7 + - - +
259P PHE* 3.5 19.2 + - - -
261P LYS* 3.5 31.3 + - - +
262P SER* 2.8 49.2 + - - +
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Residues in contact with LEU 62 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C ASP* 4.2 1.7 - - - +
29P LEU* 4.0 26.2 - - + +
32P ILE* 4.2 7.9 - - + -
33P LYS* 3.9 39.8 + - + +
36P LEU* 4.7 3.6 - - + -
58P LEU 3.1 12.1 + - - +
59P ALA 3.1 15.3 + - - +
60P PHE 3.3 9.4 - - - +
61P SER* 1.3 79.9 - - - +
63P PRO* 1.4 70.8 - - + +
64P ALA 3.6 1.2 + - - -
258P GLY 3.6 20.6 - - - +
259P PHE* 3.9 39.3 - - + -
261P LYS* 4.3 0.4 - - - -
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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
------------------------------------------------------------
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