Contacts of the helix formed by residues 29 - 47 (chain B) in PDB entry 5MJ3
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 ALA 29 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B SER 4.2 3.2 - - - +
28B PRO* 1.3 73.7 - - + +
30B TRP* 1.3 66.4 + - - +
31B THR* 3.3 4.5 - - - -
32B GLN* 3.1 42.9 + - + +
33B CYS* 3.0 17.0 + - - -
134B LEU* 4.6 7.2 - - + -
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Residues in contact with TRP 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B SER* 3.4 31.7 + - - +
28B PRO* 3.5 3.5 - - + -
29B ALA* 1.3 72.7 - - - +
31B THR* 1.3 57.9 + - - +
33B CYS* 3.2 5.5 + - - +
34B GLN* 2.8 29.3 + - - +
82B LEU* 5.1 2.0 - - + -
86B SER* 3.8 24.9 - - - -
90B LEU* 4.3 11.9 - - + -
179B VAL* 4.0 12.3 - - + -
180B PHE* 3.7 37.8 - + - +
183B GLY* 3.7 26.0 - - - -
184B ALA* 3.6 20.0 - - - +
187B LEU* 3.6 47.1 + - + +
188B SER* 4.2 11.0 - - - -
189B PRO* 5.5 1.8 - - + -
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Residues in contact with THR 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ALA* 4.8 1.9 - - - -
30B TRP* 1.3 77.4 - - + +
32B GLN* 1.3 65.5 + - - +
34B GLN* 3.4 12.1 + - - +
35B GLN* 3.0 34.2 + - - +
184B ALA* 4.1 19.3 - - + +
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Residues in contact with GLN 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ALA* 3.1 29.8 + - + +
31B THR* 1.3 83.6 + - - +
33B CYS* 1.3 61.2 + - - +
35B GLN* 3.4 6.3 + - - +
36B LEU* 3.1 29.8 + - + +
134B LEU* 3.6 24.6 - - + +
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Residues in contact with CYS 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B PRO* 3.6 22.2 - - - -
29B ALA 3.0 6.8 + - - +
30B TRP* 3.7 5.8 - - - +
32B GLN* 1.3 74.5 - - - +
34B GLN* 1.3 62.1 + - - +
36B LEU* 4.1 0.5 - - - +
37B SER* 2.8 34.1 + - - -
131B LEU* 4.1 10.7 - - + +
134B LEU* 3.4 25.8 - - - -
135B LEU* 4.0 24.9 - - - -
180B PHE* 3.4 28.2 - - + -
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Residues in contact with GLN 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A ARG* 5.2 6.9 - - - +
314A TYR* 4.9 3.2 + - - +
30B TRP 2.8 15.9 + - - +
31B THR* 3.5 11.4 - - - +
32B GLN 3.3 0.2 - - - -
33B CYS* 1.3 77.6 - - - +
35B GLN* 1.3 66.2 + - + +
37B SER* 3.2 6.3 + - - -
38B GLN* 3.0 26.7 + - + +
177B ALA 5.5 0.7 - - - +
180B PHE* 3.8 13.6 - - - +
181B ALA* 3.7 32.8 + - + +
184B ALA* 3.2 19.0 - - - +
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Residues in contact with GLN 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B THR* 3.0 22.1 + - - +
32B GLN* 3.8 7.2 - - - +
33B CYS 3.3 0.2 - - - -
34B GLN* 1.3 80.1 - - + +
36B LEU* 1.3 66.9 + - + +
38B GLN* 3.5 5.1 + - - +
39B LYS* 3.2 21.8 + - - +
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Residues in contact with LEU 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B GLN* 3.1 14.2 + - + +
33B CYS 4.1 2.5 - - - +
35B GLN* 1.3 77.0 - - + +
37B SER* 1.3 61.9 + - - +
39B LYS* 3.4 24.7 + - + +
40B LEU* 3.0 30.3 + - - +
127B SER* 5.7 2.7 - - - +
130B GLY* 4.1 25.4 - - - +
131B LEU* 4.3 12.3 - - + -
134B LEU* 3.9 25.1 - - + -
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Residues in contact with SER 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B CYS 2.8 24.5 + - - -
34B GLN* 3.2 11.4 + - - -
36B LEU* 1.3 73.9 - - - +
38B GLN* 1.3 65.1 + - - +
40B LEU* 3.2 10.5 + - - +
41B CYS* 3.1 25.3 + - - -
131B LEU* 4.3 12.5 - - - +
173B VAL* 4.7 1.5 - - - +
176B ALA* 4.5 2.5 - - - -
177B ALA* 3.5 28.0 + - - +
180B PHE* 3.6 21.0 - - - +
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Residues in contact with GLN 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ASP* 4.5 5.1 - - - +
313A ARG* 3.6 23.9 + - - +
314A TYR* 3.4 28.2 - - + -
34B GLN* 3.0 20.3 + - + +
35B GLN* 3.8 6.1 - - - +
36B LEU 3.3 0.2 - - - -
37B SER* 1.3 78.0 + - - +
39B LYS* 1.3 62.6 + - - +
41B CYS* 3.1 21.8 + - - +
42B THR* 3.1 19.1 + - - +
177B ALA* 4.5 4.9 - - - +
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Residues in contact with LYS 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B GLN 3.2 11.7 + - - +
36B LEU* 3.6 26.6 - - + +
37B SER 3.3 0.2 - - - -
38B GLN* 1.3 79.2 - - - +
40B LEU* 1.3 63.3 + - - +
42B THR* 3.2 9.0 + - - -
43B LEU* 3.0 39.1 + - + +
127B SER* 3.2 27.2 + - - +
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Residues in contact with LEU 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU 3.0 14.1 + - - +
37B SER* 3.4 11.0 - - - +
38B GLN 3.2 0.2 - - - -
39B LYS* 1.3 78.9 - - - +
41B CYS* 1.3 57.4 + - - +
43B LEU* 3.8 3.2 - - - +
44B ALA* 2.8 32.4 + - - +
97B LEU* 4.2 5.4 - - + -
124B LEU* 3.9 17.3 - - + +
127B SER* 3.5 34.8 - - - +
128B LEU* 3.7 35.4 - - + +
131B LEU* 3.6 31.2 - - + -
173B VAL* 4.2 17.7 - - + +
176B ALA* 6.2 0.9 - - + -
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Residues in contact with CYS 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A TYR* 3.6 32.1 - - - +
37B SER 3.1 9.2 + - - -
38B GLN* 3.1 17.0 + - - +
40B LEU* 1.3 77.6 - - - +
42B THR* 1.3 65.0 + - - +
44B ALA* 3.4 3.3 + - - +
45B TRP* 3.2 25.0 - - + -
173B VAL* 3.4 40.8 - - - -
174B ALA* 3.8 2.5 - - - -
177B ALA* 3.7 20.0 - - - -
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Residues in contact with THR 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B GLN* 3.1 25.9 + - - +
39B LYS* 3.6 10.1 - - - -
41B CYS* 1.3 79.2 - - - +
43B LEU* 1.3 62.2 + - + +
45B TRP* 3.3 4.4 + - - +
46B SER* 3.0 34.4 + - - +
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Residues in contact with LEU 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LYS* 3.0 36.0 + - + +
40B LEU 4.1 0.9 - - - +
42B THR* 1.3 78.3 - - + +
44B ALA* 1.3 67.7 + - - +
46B SER* 3.5 11.9 - - - +
47B ALA* 2.9 31.8 + - + +
120B PRO* 5.6 4.0 - - + +
123B GLN* 4.1 27.8 - - + +
124B LEU* 4.0 19.3 - - + +
127B SER* 3.5 27.8 - - - +
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Residues in contact with ALA 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B LEU 2.8 18.7 + - - +
41B CYS 3.8 4.9 - - - +
42B THR 3.3 0.2 - - - -
43B LEU* 1.3 75.5 - - - +
45B TRP* 1.3 60.1 + - + +
47B ALA* 4.6 2.6 + - - +
48B HIS* 5.4 2.1 + - - +
50B LEU* 4.9 0.9 - - - +
124B LEU* 3.8 23.0 - - + +
166B LEU* 4.8 8.5 - - + +
169B LEU* 4.8 4.9 - - + -
170B GLN* 3.0 38.5 + - + +
173B VAL* 4.0 17.0 - - + -
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Residues in contact with TRP 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A ASP* 5.6 0.4 - - - -
314A TYR 4.1 7.7 + - - -
315A TYR* 3.8 36.1 - + - +
316A SER* 3.4 60.9 - - - +
41B CYS* 3.2 22.8 + - - +
42B THR* 3.3 8.1 + - - +
43B LEU 3.1 0.2 - - - -
44B ALA* 1.3 80.4 - - + +
46B SER* 1.3 58.2 + - - +
47B ALA 3.6 0.2 - - - -
48B HIS 4.1 3.2 - - - +
50B LEU* 3.7 51.6 - - + +
170B GLN* 3.4 43.5 + - + +
173B VAL* 6.0 0.4 - - + +
24C TYR* 6.0 0.2 - - - -
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Residues in contact with SER 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B THR* 3.0 23.1 + - - +
43B LEU* 3.2 18.2 + - - +
45B TRP* 1.3 75.8 - - - +
47B ALA* 1.3 65.9 + - - +
48B HIS 3.3 3.8 + - - -
120B PRO* 5.2 0.3 - - - +
24C TYR* 3.4 17.7 + - - -
27C THR* 5.3 2.3 + - - -
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Residues in contact with ALA 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU* 2.9 21.9 + - + +
44B ALA 4.6 1.7 - - - +
45B TRP 3.6 0.6 - - - -
46B SER* 1.3 79.5 + - - +
48B HIS* 1.3 60.7 + - + +
120B PRO* 3.4 46.6 - - + +
121B VAL* 3.9 15.2 - - + +
124B LEU* 4.5 9.6 - - + -
166B LEU* 6.1 0.2 - - + -
24C TYR* 3.2 14.4 + - - -
114C MET* 5.0 3.6 - - - +
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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
------------------------------------------------------------
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