Contacts of the strand formed by residues 40 - 54 (chain A) in PDB entry 3MWZ
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 HIS 40 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A LYS* 2.9 31.9 - - - +
39A THR* 1.3 105.8 + - - +
41A PHE* 1.3 60.2 + - - +
68A GLU* 3.8 23.3 + - + +
69A SER 3.5 25.4 - - - +
70A THR* 3.9 9.2 + - - -
71A CYS 3.3 22.9 - - - +
72A GLU* 3.6 22.1 + - + +
73A LEU* 3.8 6.2 - - - +
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Residues in contact with PHE 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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29A SER* 3.6 30.1 - - - -
32A SER* 3.7 3.1 - - - -
33A ALA* 4.1 7.9 - - + -
40A HIS* 1.3 74.8 - - - +
42A ASP* 1.3 61.7 + - - +
68A GLU* 3.8 1.0 - - - -
69A SER* 2.7 38.7 + - - +
71A CYS* 2.9 17.1 + - + -
72A GLU 3.4 17.3 - - - -
73A LEU* 3.6 28.3 - - + -
75A SER* 3.3 27.1 - - - -
77A TYR* 3.6 49.1 - + + -
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Residues in contact with ASP 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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28A THR* 3.5 15.8 - - + +
29A SER* 4.3 0.2 - - - -
31A TRP* 3.5 11.1 - - + -
32A SER* 3.0 20.2 + - - +
38A LYS* 2.8 33.7 + - - -
40A HIS 3.6 0.2 + - - -
41A PHE* 1.3 83.0 - - - +
43A THR* 1.3 60.9 + - - +
66A VAL* 3.6 15.3 - - + -
67A ALA 3.5 3.1 - - - +
68A GLU* 3.3 16.3 + - - +
77A TYR* 3.7 7.3 + - - -
91A ARG* 2.6 37.9 + - - -
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Residues in contact with THR 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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25A HIS* 3.6 8.3 - - - -
28A THR* 3.9 5.2 - - - -
42A ASP* 1.3 74.7 - - - +
44A VAL* 1.3 73.8 + - - +
45A VAL* 5.1 0.7 - - + +
66A VAL* 3.3 8.7 - - - +
67A ALA 2.8 38.9 + - - +
69A SER* 3.8 8.3 - - - -
77A TYR* 2.7 24.8 + - - -
79A LYS 5.0 1.2 + - - -
82A CYS* 3.4 27.7 + - - +
83A GLN* 4.2 1.9 - - - -
84A ALA* 3.6 25.4 - - + +
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Residues in contact with VAL 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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21A LEU* 4.2 15.3 - - + +
24A ALA* 3.5 37.9 - - + +
25A HIS* 3.8 28.2 + - + +
28A THR* 3.5 15.3 - - + +
43A THR* 1.3 81.8 + - - +
45A VAL* 1.3 66.5 + - - +
46A GLU* 3.8 25.8 - - - +
47A VAL* 4.2 8.7 - - + +
64A LEU* 4.4 7.4 - - + -
65A LYS 3.8 4.3 - - - +
66A VAL* 4.8 0.9 - - - +
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Residues in contact with VAL 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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43A THR* 3.6 1.5 + - + +
44A VAL* 1.3 75.3 - - - +
46A GLU* 1.3 63.2 + - + +
65A LYS* 2.8 26.2 + - + +
66A VAL 4.4 1.3 - - - -
67A ALA* 4.0 30.5 - - + +
84A ALA* 4.3 13.0 - - + +
90A GLN* 4.5 22.4 - - + +
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Residues in contact with GLU 46 (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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14A ASN* 4.8 7.5 + - - +
21A LEU* 6.1 1.1 - - - -
44A VAL* 3.6 7.5 - - - +
45A VAL* 1.3 87.9 - - + +
47A VAL* 1.3 72.9 + - - +
48A MSE 3.4 24.5 + - + +
64A LEU* 3.4 3.1 - - - -
65A LYS* 2.9 33.6 + - + +
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Residues in contact with VAL 47 (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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14A ASN* 2.8 39.8 + - + +
20A TYR* 4.4 5.8 - - + +
21A LEU* 3.9 30.4 - - + +
24A ALA* 3.9 27.6 - - + -
44A VAL* 4.2 1.1 - - + +
46A GLU* 1.3 77.0 - - - +
48A MSE 1.3 60.2 + - - +
49A LYS 4.0 8.5 - - - +
50A VAL* 3.5 31.6 - - + -
62A LEU* 5.0 3.6 - - + -
63A THR 4.0 2.0 - - - -
64A LEU* 3.9 11.0 - - + -
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Residues in contact with MSE 48 (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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11A GLU* 5.4 1.0 - - - +
14A ASN* 5.2 2.7 + - - -
46A GLU* 4.0 31.6 - - + +
47A VAL* 1.3 75.2 - - - +
49A LYS* 1.3 59.6 + - + +
63A THR* 2.7 21.0 + - + +
64A LEU 3.6 26.2 - - - +
65A LYS* 3.8 26.7 - - + +
92A THR* 3.7 23.3 - - + +
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Residues in contact with LYS 49 (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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11A GLU* 3.7 37.8 + - - +
14A ASN* 6.1 0.7 - - - -
47A VAL* 3.6 2.5 - - - +
48A MSE 1.3 79.7 - - + +
50A VAL* 1.3 67.3 + - - +
51A GLU* 4.0 35.5 + - + +
61A ARG 4.5 0.7 - - - -
62A LEU* 3.5 3.8 - - - -
63A THR* 2.9 47.6 + - + +
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Residues in contact with VAL 50 (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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11A GLU* 3.4 9.2 - - - +
12A ARG* 2.8 45.6 + - + +
14A ASN* 4.1 13.7 - - + +
20A TYR* 3.6 54.5 - - + -
47A VAL* 3.5 24.2 - - + -
49A LYS* 1.3 79.4 - - - +
51A GLU* 1.3 66.9 + - - +
52A THR* 4.4 4.0 - - + -
61A ARG 3.7 2.9 - - - -
62A LEU* 3.9 9.9 - - + -
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Residues in contact with GLU 51 (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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9A TYR* 3.6 21.4 - - + +
10A ARG 3.2 8.7 - - - +
11A GLU* 4.4 7.2 - - + +
49A LYS* 4.0 34.7 + - + +
50A VAL* 1.3 80.8 - - - +
52A THR* 1.3 67.2 + - - +
60A TYR* 3.7 0.2 - - - -
61A ARG* 2.8 81.7 + - + +
63A THR* 4.6 6.1 + - - -
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Residues in contact with THR 52 (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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8A GLY 3.9 0.9 - - - +
9A TYR* 3.5 5.0 - - - -
10A ARG* 2.9 35.2 + - - +
12A ARG* 3.0 45.1 + - + +
20A TYR* 4.4 6.3 - - + +
50A VAL* 4.4 2.2 - - + -
51A GLU* 1.3 81.2 - - - +
53A GLN* 1.3 61.4 + - - +
54A THR* 4.8 3.2 + - - -
58A THR* 4.1 9.2 - - - -
59A ASN 3.1 7.6 - - - -
60A TYR* 3.4 33.7 - - + -
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Residues in contact with GLN 53 (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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3A LEU* 3.6 14.9 - - + +
5A LEU* 3.1 37.6 + - + +
7A GLY 2.7 25.3 + - - -
8A GLY* 3.6 23.3 - - - +
9A TYR* 3.5 30.8 - - + +
52A THR* 1.3 71.9 - - - +
54A THR* 1.3 62.0 + - - +
55A VAL* 6.5 0.2 - - + -
58A THR* 3.2 3.6 - - - +
59A ASN* 2.9 57.9 + - + +
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Residues in contact with THR 54 (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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3A LEU* 4.3 0.2 - - - -
5A LEU* 5.9 0.7 - - - +
8A GLY 5.3 0.4 + - - -
12A ARG* 5.5 2.9 + - - -
52A THR* 4.8 3.8 + - - -
53A GLN* 1.3 75.8 + - - +
55A VAL* 1.3 80.6 + - - +
56A ALA 4.4 5.2 - - - +
57A GLY 3.4 6.5 - - - +
58A THR* 2.9 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
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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