Contacts of the strand formed by residues 22 - 31 (chain D) in PDB entry 3MDY
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 THR 22 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20D GLY 4.0 0.8 + - - -
21D GLN* 1.3 69.7 - - - +
23D CYS* 1.3 63.7 + - - +
24D VAL 3.8 0.5 + - - -
48D LYS* 3.8 37.9 - - + -
49D PHE 3.6 11.4 - - - +
50D MET* 3.9 22.2 - - - +
107D LEU* 3.5 4.7 - - - -
108D GLU* 2.8 55.6 + - + +
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Residues in contact with CYS 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D PRO* 3.8 29.4 - - - -
21D GLN 4.2 6.5 - - - -
22D THR* 1.3 71.7 - - - +
24D VAL* 1.3 60.9 + - - +
25D VAL* 4.5 0.9 - - + -
47D PHE 3.6 1.7 - - - +
48D LYS* 3.2 5.2 - - - -
49D PHE* 2.8 70.6 + - + +
51D LEU* 4.7 6.7 - - - -
64D VAL* 4.2 9.4 - - + -
104D LEU* 4.1 11.2 - - + -
106D LYS 3.9 4.3 - - - -
107D LEU* 3.9 7.9 - - - -
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Residues in contact with VAL 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D THR* 4.6 0.4 - - + -
23D CYS* 1.3 74.5 - - - +
25D VAL* 1.3 59.8 + - - +
46D PRO* 3.6 29.8 - - + -
47D PHE 3.5 2.7 - - - -
48D LYS* 3.8 26.2 - - + +
104D LEU* 3.7 2.3 - - - +
105D LEU* 2.9 34.1 + - + +
106D LYS* 2.9 29.7 + - + +
108D GLU* 3.6 39.3 - - + +
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Residues in contact with VAL 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D CYS* 4.5 1.1 - - + -
24D VAL* 1.3 79.5 - - - +
26D HIS* 1.3 61.5 + - - +
27D TYR* 4.4 4.3 - - + -
40D SER* 4.1 0.2 + - - -
46D PRO* 3.3 6.1 - - - +
47D PHE* 2.8 49.2 + - + +
49D PHE* 4.2 17.7 - - + -
60D TRP* 3.7 32.1 - - + -
64D VAL* 4.4 6.1 - - + -
102D VAL* 4.0 17.5 - - + -
103D GLU 3.2 14.1 - - - +
104D LEU* 4.0 15.9 - - + -
105D LEU* 3.8 6.1 - - - -
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Residues in contact with HIS 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D VAL* 1.3 73.7 - - - +
27D TYR* 1.3 61.2 + - - +
40D SER* 2.8 43.2 + - - -
41D ARG* 3.6 48.1 + - + +
44D ASN* 4.3 12.0 + - - -
45D LYS 3.8 5.2 - - - -
46D PRO* 3.7 27.4 - - + +
101D ASP 3.7 0.5 - - - +
102D VAL* 3.4 3.8 - - - +
103D GLU* 2.9 32.2 + - - +
105D LEU* 3.6 29.7 - - + +
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Residues in contact with TYR 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193C PRO* 4.4 1.2 - - - +
195C LEU* 3.5 21.8 + - + +
196C VAL 4.9 0.5 + - - -
25D VAL* 4.4 0.9 - - + -
26D HIS* 1.3 76.1 - - - +
28D THR* 1.3 70.0 + - - +
29D GLY 4.1 4.9 - - - -
38D ASP* 2.4 47.4 + - + -
39D SER* 3.3 3.1 + - - -
40D SER* 2.8 49.0 + - - -
41D ARG* 4.0 5.1 + - - +
43D ARG* 3.0 18.2 + - - -
47D PHE* 3.6 32.6 - + + -
60D TRP* 3.8 35.0 - + + -
100D PHE* 4.2 6.1 - + + -
101D ASP 3.1 9.2 - - - +
102D VAL* 4.3 7.6 - - + -
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Residues in contact with THR 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D TYR* 1.3 78.4 + - - +
29D GLY* 1.3 63.0 + - - +
30D MET* 4.2 15.4 - - + +
36D LYS* 3.8 35.6 - - + -
38D ASP 3.6 4.9 - - - +
39D SER* 3.5 11.1 + - - +
41D ARG* 4.3 12.5 + - - -
99D VAL 3.7 1.0 - - - +
100D PHE* 3.3 3.9 - - - -
101D ASP* 2.9 43.0 + - - +
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Residues in contact with GLY 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D TYR* 4.1 2.0 - - - -
28D THR* 1.3 71.9 - - - +
30D MET* 1.3 63.0 + - - +
36D LYS* 3.4 6.2 - - - +
37D PHE* 2.9 40.2 + - - -
38D ASP 2.9 15.1 + - - +
99D VAL 3.5 5.2 - - - -
100D PHE* 3.6 18.7 - - - -
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Residues in contact with MET 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D THR* 4.2 22.2 - - + +
29D GLY* 1.3 77.5 - - - +
31D LEU* 1.3 68.8 + - - +
34D GLY* 3.8 22.7 - - - +
35D LYS 3.2 8.7 - - - +
36D LYS* 4.0 11.2 - - + -
37D PHE* 3.3 12.3 - - - -
98D LEU* 3.7 1.7 - - - -
99D VAL* 2.8 61.3 + - + +
101D ASP* 4.5 14.6 - - + -
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Residues in contact with LEU 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D MET* 1.3 82.1 - - - +
32D GLU* 1.3 65.4 + - - +
33D ASP* 3.1 23.1 - - - +
34D GLY* 3.1 10.5 + - - -
35D LYS* 2.9 44.7 + - + +
37D PHE* 3.9 17.9 - - + -
91D ILE 4.2 4.9 - - - +
92D ILE* 3.9 16.8 - - + -
93D PRO* 4.0 30.5 - - + -
96D ALA* 4.8 2.7 - - + -
97D THR 4.2 4.9 - - - +
98D LEU* 4.0 9.2 - - + -
99D VAL* 4.3 6.3 - - - +
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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