Contacts of the helix formed by residues 21 - 35 (chain J) in PDB entry 6MZL
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 21 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20J LEU* 1.3 86.4 - - + +
22J PRO* 1.3 63.3 - - + +
23J GLU* 3.4 9.9 - - - +
24J TYR* 3.1 26.5 + - + -
25J ALA* 2.6 32.7 + - - +
63J LEU* 3.7 21.3 - - + -
97J SER* 3.3 23.6 - - - +
98J THR* 4.4 0.2 - - - -
99J VAL* 4.4 17.5 - - + +
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Residues in contact with PRO 22 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
759A GLU* 6.6 0.2 - - + -
760A THR* 4.3 14.8 - - + -
20J LEU 4.3 1.8 - - - +
21J PRO* 1.3 86.5 - - + +
23J GLU* 1.3 64.5 + - - +
25J ALA* 3.7 7.9 - - + +
26J SER* 2.9 33.8 + - - -
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Residues in contact with GLU 23 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21J PRO* 4.1 7.8 - - - +
22J PRO* 1.3 83.3 - - - +
24J TYR* 1.3 90.4 + - + +
26J SER* 3.3 7.1 + - - -
27J THR* 3.0 31.7 + - - -
30J ARG* 5.0 0.2 + - - -
99J VAL* 5.4 5.7 - - - +
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Residues in contact with TYR 24 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20J LEU* 4.2 5.2 - - + -
21J PRO* 3.1 28.6 + - + +
23J GLU* 1.3 96.7 - - + +
25J ALA* 1.3 59.8 + - - +
27J THR* 3.4 5.6 + - - -
28J VAL* 2.9 35.2 + - - +
58J VAL* 4.0 28.7 - - + -
61J VAL* 3.7 34.3 - - + +
63J LEU* 3.7 38.9 - - + +
99J VAL* 4.4 13.4 - - + +
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Residues in contact with ALA 25 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
759A GLU* 3.5 22.7 - - + +
760A THR* 3.7 17.7 - - + +
762A PHE* 3.8 6.8 - - + -
20J LEU* 3.9 17.6 - - + +
21J PRO 2.6 20.5 + - - +
22J PRO* 3.7 9.2 - - + +
24J TYR* 1.3 73.2 - - - +
26J SER* 1.3 56.4 + - - +
28J VAL* 4.8 0.2 - - - -
29J ARG* 2.8 32.5 + - - +
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Residues in contact with SER 26 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
759A GLU* 6.1 1.4 - - - +
22J PRO* 2.9 22.7 + - - +
23J GLU* 3.7 6.7 - - - -
25J ALA* 1.3 75.2 - - - +
27J THR* 1.3 60.1 + - - +
29J ARG* 3.4 8.8 + - - +
30J ARG* 2.9 51.2 + - - +
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Residues in contact with THR 27 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23J GLU 3.0 18.4 + - - -
24J TYR* 3.8 7.8 - - - -
26J SER* 1.3 75.5 - - - +
28J VAL* 1.3 58.1 + - - +
30J ARG* 3.3 27.3 + - - +
31J ALA* 3.0 26.0 + - - +
42J ARG* 3.5 25.3 + - - +
58J VAL* 4.8 9.2 - - + -
59J ASP* 4.0 13.2 - - - +
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Residues in contact with VAL 28 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762A PHE* 3.6 23.8 - - + -
773A ILE* 4.4 0.2 - - + -
20J LEU* 4.0 8.7 - - + -
24J TYR 2.9 20.7 + - - +
27J THR* 1.3 76.2 - - + +
29J ARG* 1.3 56.7 + - - +
31J ALA* 3.2 6.6 + - - +
32J VAL* 2.8 35.6 + - + +
39J LEU* 4.4 7.0 - - + -
42J ARG* 5.4 1.1 - - + +
43J LEU* 3.8 31.6 - - + -
58J VAL* 3.8 34.3 - - + -
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Residues in contact with ARG 29 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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757A MET* 5.5 1.0 + - - +
758A PRO 3.6 6.7 + - - -
759A GLU* 3.0 63.5 + - - +
761A ASP 4.0 3.4 + - - -
762A PHE* 3.3 29.4 - - + -
775A GLU* 3.3 33.3 + - - +
776A LEU 5.3 4.0 + - - -
777A VAL* 4.6 11.1 - - - +
25J ALA 2.8 21.0 + - - +
26J SER* 3.6 9.0 - - - +
27J THR 3.2 0.2 - - - -
28J VAL* 1.3 77.9 - - - +
30J ARG* 1.3 57.1 + - + +
32J VAL* 3.3 4.1 + - - +
33J GLN* 2.9 52.5 + - + +
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Residues in contact with ARG 30 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23J GLU 5.0 0.2 + - - -
26J SER* 2.9 38.2 + - - +
27J THR* 3.3 34.4 + - - +
29J ARG* 1.3 76.2 - - + +
31J ALA* 1.3 57.2 + - - +
33J GLN* 3.8 11.3 - - - +
34J SER* 2.9 30.0 + - - -
42J ARG* 6.3 0.2 - - - +
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Residues in contact with ALA 31 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27J THR 3.0 12.7 + - - +
28J VAL* 3.2 10.1 + - - +
30J ARG* 1.3 76.9 - - - +
32J VAL* 1.3 56.9 + - - +
34J SER* 2.6 22.1 + - - -
35J GLY* 3.1 12.0 + - - -
36J HIS* 4.1 3.8 + - - +
39J LEU* 3.7 31.6 - - + +
42J ARG* 3.6 28.9 - - - +
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Residues in contact with VAL 32 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638A PRO* 5.8 2.8 - - + +
640A LEU* 4.5 8.3 - - - +
762A PHE* 4.9 5.8 - - + -
773A ILE* 4.2 26.5 - - + +
774A ARG* 4.6 4.7 - - - -
775A GLU* 3.8 39.3 - - + +
28J VAL* 2.8 22.8 + - + +
29J ARG* 3.8 7.0 - - - +
31J ALA* 1.3 74.6 - - - +
33J GLN* 1.3 63.0 + - - +
35J GLY* 3.2 13.7 + - - -
39J LEU* 3.8 24.0 - - + -
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Residues in contact with GLN 33 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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640A LEU* 4.0 10.7 - - - +
775A GLU* 2.8 39.8 + - - +
29J ARG* 2.9 35.9 + - - +
30J ARG* 4.0 10.3 - - - +
32J VAL* 1.3 76.1 - - - +
34J SER* 1.3 60.8 + - - +
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Residues in contact with SER 34 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640A LEU* 4.1 5.9 - - - +
30J ARG 2.9 17.7 + - - -
31J ALA* 2.6 25.3 + - - -
33J GLN* 1.3 79.1 - - - +
35J GLY* 1.3 60.2 + - - +
36J HIS* 3.3 36.4 + - - +
42J ARG* 5.2 2.8 + - - -
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Residues in contact with GLY 35 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638A PRO* 4.2 14.7 - - - +
640A LEU* 3.7 24.8 - - - +
641A LYS* 4.8 16.1 - - - +
31J ALA 3.1 6.7 + - - -
32J VAL 3.2 12.2 + - - -
34J SER* 1.3 78.5 + - - +
36J HIS* 1.3 65.3 + - - +
37J VAL* 3.7 2.1 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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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