Contacts of the helix formed by residues 29 - 46 (chain A) in PDB entry 3M6L
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 PRO 29 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A SER 5.7 0.9 - - - +
18A ALA* 5.1 4.3 - - - -
21A VAL* 4.1 17.0 - - + -
27A GLY 3.5 5.8 - - - +
28A HIS* 1.4 85.3 - - - +
30A GLY* 1.3 63.6 + - - +
31A ALA 3.5 1.1 - - - -
32A PRO* 3.4 4.9 - - + +
33A LEU* 3.1 32.4 + - + +
255A SER 3.3 15.0 - - - +
256A HIS 4.0 1.1 - - - +
258A ALA 3.1 30.3 - - - +
259A PRO* 4.5 0.7 - - + -
260A LEU* 3.7 39.7 - - + +
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Residues in contact with GLY 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A HIS 3.6 1.0 - - - -
29A PRO* 1.3 78.3 - - - +
31A ALA* 1.3 57.7 + - - +
34A GLY* 3.0 23.4 + - - -
242A ILE* 3.6 23.6 - - - +
243A ALA* 3.0 19.8 + - - -
255A SER* 2.9 23.6 + - - -
256A HIS* 4.3 1.0 + - - -
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Residues in contact with ALA 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A HIS 5.1 0.6 - - - -
30A GLY* 1.3 71.3 - - - +
32A PRO* 1.4 76.4 - - + +
34A GLY* 3.2 1.7 + - - +
35A LEU* 2.9 36.3 + - + +
67A HIS* 3.9 15.9 - - + +
68A ALA* 4.0 12.1 - - + -
180A ASP* 4.7 8.5 - - - +
182A ASN* 5.4 0.4 - - - +
242A ILE* 4.2 1.7 - - - +
256A HIS* 5.2 2.6 + - - +
5001A TPP 3.2 26.9 + - - +
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Residues in contact with PRO 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ARG* 5.4 1.1 - - - -
17A SER* 3.7 31.6 - - - +
28A HIS 3.1 28.0 - - - +
29A PRO* 3.4 7.9 - - + +
31A ALA* 1.4 95.2 - - + +
33A LEU* 1.3 62.6 + - - +
35A LEU 3.3 0.9 + - - -
36A ALA* 3.1 26.2 + - - +
67A HIS 4.9 0.2 - - - +
68A ALA* 4.2 15.0 - - + -
70A ALA* 4.6 3.1 - - + -
71A LEU* 3.9 32.6 - - + +
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Residues in contact with LEU 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ARG* 3.0 72.4 + - + +
15A PHE* 6.0 4.5 - - + -
17A SER* 4.7 0.2 - - - -
18A ALA* 4.5 11.2 - - + +
29A PRO* 3.1 21.2 + - + +
32A PRO* 1.3 85.0 - - + +
34A GLY* 1.3 59.2 + - - +
35A LEU 3.5 0.2 + - - -
36A ALA 3.7 1.6 + - - -
243A ALA* 3.6 14.4 - - + +
244A LYS* 3.5 23.2 - - - +
245A GLY 4.8 1.1 - - - -
246A ALA* 3.7 28.0 - - + +
260A LEU* 4.0 14.4 - - + -
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Residues in contact with GLY 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A GLY 3.0 14.4 + - - -
31A ALA* 3.2 3.8 + - - -
33A LEU* 1.3 78.6 - - - +
35A LEU* 1.3 58.7 + - - +
36A ALA 3.5 0.2 - - - -
37A ASP 4.9 0.3 + - - -
38A ILE* 4.7 1.9 - - - +
180A ASP* 4.7 2.5 - - - -
214A GLY 4.7 1.2 - - - +
215A HIS* 3.4 20.7 + - - -
240A THR* 3.6 19.5 - - - +
241A THR 3.6 23.6 - - - -
242A ILE* 4.9 1.1 - - - -
243A ALA 4.1 0.6 - - - +
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Residues in contact with LEU 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ALA* 2.9 25.3 + - + +
32A PRO 3.8 0.2 - - - -
34A GLY* 1.3 74.6 - - - +
36A ALA* 1.3 58.9 + - - +
37A ASP 3.3 2.5 - - - -
38A ILE* 3.2 26.6 + - + +
39A LEU* 3.0 26.5 + - - +
63A PHE* 5.2 1.3 - - + -
68A ALA* 4.3 15.0 - - + -
71A LEU* 3.5 22.2 - - + -
149A LEU* 4.5 33.0 - - + -
150A CYS 6.1 0.2 - - - +
178A ILE* 5.7 2.2 - - + +
180A ASP* 3.7 37.0 - - + +
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Residues in contact with ALA 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ALA* 3.5 25.1 - - - +
13A LEU* 4.0 7.0 - - + +
14A ARG* 3.6 26.0 - - + +
32A PRO 3.1 15.4 + - - +
33A LEU 3.7 4.0 + - - +
34A GLY 3.5 1.8 - - - -
35A LEU* 1.3 75.2 - - - +
37A ASP* 1.4 60.9 + - - +
39A LEU* 4.6 1.1 - - - +
40A SER* 2.8 30.1 + - - -
71A LEU* 4.4 8.5 - - + -
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Residues in contact with ASP 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ALA* 3.1 4.0 - - - +
14A ARG* 2.9 26.2 + - - +
34A GLY 4.9 0.6 + - - -
35A LEU 3.3 0.6 - - - -
36A ALA* 1.4 74.7 - - - +
38A ILE* 1.3 65.6 + - - +
40A SER* 3.5 1.9 + - - -
41A VAL* 3.2 26.7 + - - +
214A GLY 3.6 14.1 - - - +
215A HIS* 2.8 36.1 + - - +
217A TYR* 2.5 42.3 + - + -
220A ILE* 3.9 5.6 - - + -
244A LYS* 4.6 1.0 - - - +
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Residues in contact with ILE 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A GLY 4.7 2.9 - - - +
35A LEU* 3.2 24.5 + - + +
37A ASP* 1.3 76.3 - - - +
39A LEU* 1.3 61.7 + - - +
41A VAL* 3.3 3.3 + - - +
42A LEU* 2.9 27.9 + - + +
149A LEU* 4.3 15.7 - - + -
178A ILE* 4.2 28.5 - - + -
180A ASP* 5.2 0.7 - - - +
212A ILE* 5.4 0.9 - - + -
214A GLY* 3.6 15.0 + - - +
220A ILE* 3.9 23.7 - - + +
224A LEU* 6.0 0.7 - - + -
238A ALA* 3.7 30.3 - - + -
240A THR* 4.0 19.1 - - + -
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Residues in contact with LEU 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LEU* 4.2 8.5 - - + -
35A LEU 3.0 15.4 + - - +
36A ALA 4.1 3.1 - - - +
38A ILE* 1.3 79.8 - - + +
40A SER* 1.3 63.6 + - - +
42A LEU* 3.2 22.5 + - + -
43A SER* 3.0 22.9 + - - +
46A LEU* 6.2 0.4 - - + -
61A LEU* 4.6 15.0 - - + -
63A PHE* 4.1 14.8 - - + -
71A LEU* 3.5 39.5 - - + -
75A PHE* 3.8 42.0 - - + -
149A LEU* 4.9 5.8 - - + -
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Residues in contact with SER 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LEU* 4.0 17.7 - - - -
9A GLN* 3.6 6.2 - - - +
10A ALA* 3.1 33.0 + - - -
13A LEU* 3.4 11.8 - - - +
36A ALA 2.8 18.9 + - - -
37A ASP* 3.6 5.6 - - - -
39A LEU* 1.3 76.7 - - - +
41A VAL* 1.3 59.3 + - - +
43A SER* 2.7 26.4 + - - -
44A TYR* 3.3 10.2 - - - -
217A TYR* 5.0 1.6 - - - -
290A PHE* 4.8 3.1 - - - -
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Residues in contact with VAL 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MSE 3.9 9.4 - - + -
6A LEU* 4.2 8.1 - - + -
37A ASP 3.2 15.2 + - - +
38A ILE 3.9 0.9 - - - +
40A SER* 1.3 73.5 - - - +
42A LEU* 1.3 67.3 + - - +
44A TYR* 3.0 24.7 + - - +
45A HIS* 3.4 4.4 - - + -
217A TYR* 3.7 37.0 - - + +
220A ILE* 3.7 27.8 - - + -
221A ASN* 3.8 30.1 - - + +
224A LEU* 4.0 6.7 - - + -
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Residues in contact with LEU 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ILE* 2.9 19.7 + - + +
39A LEU* 3.2 19.5 + - + +
41A VAL* 1.3 76.6 - - - +
43A SER* 1.3 57.4 + - - +
45A HIS* 2.9 21.6 + - + +
46A LEU* 3.0 21.2 + - + +
61A LEU* 4.1 26.7 - - + -
147A TYR* 3.7 41.1 - - + -
149A LEU* 4.5 8.1 - - + -
178A ILE* 4.3 16.8 - - + -
224A LEU* 4.0 24.0 - - + +
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Residues in contact with SER 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A LEU* 3.0 12.9 + - - +
40A SER 2.7 20.7 + - - -
41A VAL 3.1 0.4 - - - -
42A LEU* 1.3 77.2 - - - +
44A TYR* 1.3 58.1 + - - +
45A HIS 3.6 0.2 + - - -
46A LEU* 4.0 13.7 + - - +
48A HIS* 5.0 4.4 - - - -
75A PHE* 3.7 31.2 - - - -
290A PHE* 4.0 10.0 - - - -
2001A GOL 2.7 44.1 + - - -
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Residues in contact with TYR 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MSE 3.4 41.3 - - + -
5A ILE* 4.0 5.2 - - - +
6A LEU* 3.4 26.2 - - + +
9A GLN* 2.6 24.6 + - - -
40A SER 3.3 15.5 - - - -
41A VAL 3.0 11.0 + - - +
43A SER* 1.3 76.4 - - - +
45A HIS* 1.3 66.0 + - + +
46A LEU 5.1 0.8 - - - +
47A LYS* 5.1 3.8 + - - -
289A ARG* 3.1 34.6 + - - +
2001A GOL 3.7 31.6 + - - -
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Residues in contact with HIS 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MSE 5.3 0.4 - - - -
41A VAL* 3.4 17.9 - - + +
42A LEU* 2.9 11.9 + - + +
44A TYR* 1.3 86.6 + - + +
46A LEU* 1.3 63.2 + - - +
47A LYS* 3.4 20.2 + - - +
59A ASP* 3.8 5.6 - - - +
147A TYR* 4.1 14.7 + - - +
221A ASN* 2.8 28.3 + - - -
224A LEU* 3.7 29.6 - - + +
225A GLU* 3.2 32.1 - - + -
228A LYS* 2.8 30.6 + - - +
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Residues in contact with LEU 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 6.2 0.7 - - + -
42A LEU* 3.0 22.1 + - + +
43A SER* 4.0 7.9 + - - +
44A TYR 3.7 1.3 - - - -
45A HIS* 1.3 77.2 - - - +
47A LYS* 1.3 59.8 + - - +
48A HIS* 3.4 46.8 + - + +
59A ASP* 3.6 20.2 - - + +
61A LEU* 4.3 31.4 - - + -
75A PHE* 4.0 21.5 - - + -
147A TYR* 3.7 29.6 - - + -
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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