Contacts of the strand formed by residues 34 - 43 (chain E) in PDB entry 3M4D
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 MET 34 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E THR 3.7 0.3 - - - +
28E TYR* 3.3 7.3 - - - -
29E ASP* 2.8 38.8 + - + -
32E ASN* 3.5 21.8 - - + +
33E GLY* 1.3 83.6 - - - +
35E HIS* 1.3 60.1 + - - +
36E LYS* 3.6 15.3 + - + +
60E THR 3.6 5.2 - - - +
61E ILE* 4.1 17.9 - - + -
249E TYR* 3.6 19.5 - - - +
250E GLU 3.9 3.4 - - - +
251E ARG* 3.8 25.8 - - + +
276E ASP 3.5 24.5 - - - +
278E SER* 3.6 25.6 - - - -
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Residues in contact with HIS 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D ILE 2.9 27.7 + - - -
99D SER* 3.7 14.6 - - - -
101D TYR* 2.7 41.0 + + - +
160D PRO* 3.6 20.8 + - + +
161D THR 3.6 24.5 + - - -
162D ASP* 3.7 4.3 - - + -
26E VAL* 3.4 19.3 - - + +
27E THR 3.9 1.8 - - - -
28E TYR* 3.7 6.7 - + + -
34E MET* 1.3 69.6 - - - +
36E LYS* 1.3 59.9 + - - +
37E LYS* 4.6 3.6 - - + -
58E LYS 4.0 0.7 - - - +
59E GLY* 3.2 13.2 - - - -
60E THR 2.8 41.0 + - - +
249E TYR* 4.2 2.1 - - - -
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Residues in contact with LYS 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E LEU 3.7 1.0 - - - +
26E VAL* 3.4 4.4 - - - +
27E THR* 2.8 62.5 + - - +
29E ASP* 4.7 5.6 - - - +
34E MET* 3.8 12.6 - - + +
35E HIS* 1.3 76.7 - - - +
37E LYS* 1.3 60.7 + - - +
38E VAL* 5.7 0.2 - - - -
247E VAL* 4.8 2.5 + - + -
249E TYR* 3.6 49.6 - - + -
278E SER* 2.8 40.2 + - - +
279E SER 4.1 2.6 + - - -
280E GLU* 3.8 25.8 + - - +
282E TYR* 5.1 9.1 + - - +
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Residues in contact with LYS 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ASN* 4.8 3.2 + - - -
99D SER* 2.8 40.5 + - - +
100D ASP* 3.9 12.0 + - - +
231D VAL* 5.4 0.4 - - - +
24E ASP* 2.7 28.2 + - - +
25E LEU 3.3 3.8 - - - +
26E VAL* 3.6 21.8 - - + -
35E HIS* 4.0 3.5 + - + -
36E LYS* 1.3 75.2 - - - +
38E VAL* 1.3 75.7 + - - +
39E PHE* 3.7 8.5 - - - +
57E THR* 3.6 4.0 - - - -
58E LYS* 2.9 63.0 + - + -
59E GLY* 4.1 12.8 - - - +
249E TYR* 3.7 3.7 + - - -
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Residues in contact with VAL 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E GLY 3.7 0.9 - - - +
24E ASP* 3.4 4.9 - - - -
25E LEU* 2.9 42.5 + - + +
36E LYS* 5.7 0.4 - - + -
37E LYS* 1.3 81.8 - - - +
39E PHE* 1.3 66.1 + - - +
40E TYR* 4.4 5.3 - - + +
55E ILE* 3.8 24.7 - - + -
56E ARG 3.4 4.0 - - - +
57E THR* 4.8 12.6 - - + -
247E VAL* 5.0 6.1 - - + -
249E TYR* 5.7 1.3 - - + +
282E TYR* 3.5 35.4 - - + +
291E MET* 4.1 21.1 - - + -
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Residues in contact with PHE 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ASN* 3.9 38.6 - - + +
12D THR* 3.3 26.5 - - - -
14D ILE* 3.2 36.1 - - + -
48D HIS* 3.5 7.6 - + - -
22E THR* 4.2 5.8 - - - -
23E GLY 3.2 13.7 - - - -
24E ASP* 3.7 14.4 - - - -
37E LYS* 3.7 17.9 - - + +
38E VAL* 1.3 73.5 - - - +
40E TYR* 1.3 58.9 + - - +
41E SER* 3.6 16.6 - - - -
54E VAL 3.7 1.2 - - - +
56E ARG* 2.8 55.6 + - + +
58E LYS* 5.0 0.7 - - + -
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Residues in contact with TYR 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D ASN* 3.8 23.6 + - - +
21E LYS 4.2 2.7 - - - -
22E THR* 3.2 10.2 + - - -
23E GLY* 2.9 58.1 + - - -
24E ASP 4.2 0.4 - - - -
25E LEU* 4.3 9.9 - - + -
38E VAL* 4.5 7.2 - - + -
39E PHE* 1.3 76.2 - - - +
41E SER* 1.3 70.6 + - - +
42E PHE* 3.6 34.5 - + - -
53E LEU* 4.0 4.3 - - + -
54E VAL 3.2 8.7 - - - +
55E ILE* 4.8 2.0 - - + -
289E GLU 4.5 2.5 + - - -
290E GLU* 3.8 8.9 - - - +
291E MET* 3.4 62.2 + - + -
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Residues in contact with SER 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D THR* 3.3 39.7 - - - -
20E VAL* 4.1 6.1 - - - -
21E LYS 3.4 5.6 - - - -
22E THR* 3.5 13.9 - - - +
39E PHE* 3.6 8.0 - - - -
40E TYR* 1.3 79.7 + - - +
42E PHE* 1.3 60.9 + - - +
43E ILE* 3.7 2.4 + - - -
52E LEU 3.8 0.2 - - - +
53E LEU* 3.3 6.0 - - - -
54E VAL* 2.8 43.6 + - - +
56E ARG* 4.5 1.2 + - - -
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Residues in contact with PHE 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E THR 4.5 0.7 - - - +
20E VAL* 3.4 9.4 - - - +
21E LYS* 2.8 30.6 + - + +
40E TYR* 3.6 29.2 - + - -
41E SER* 1.3 71.4 - - - +
43E ILE* 1.3 60.1 + - - +
44E ASP 4.0 1.3 + - - -
52E LEU 3.3 6.7 - - - -
53E LEU* 3.7 19.3 - - + -
284E ILE* 3.8 24.0 - - + -
285E ASP 4.0 9.0 - - - -
286E TRP* 3.9 25.1 - + - -
289E GLU* 3.3 57.8 - - + +
290E GLU 3.3 23.3 - - - -
291E MET* 4.0 2.0 - - + -
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Residues in contact with ILE 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D ILE* 3.7 35.2 - - + -
11D THR* 4.0 16.8 - - + -
12D THR* 4.2 5.4 - - + -
14E ILE* 4.1 14.4 - - + -
15E GLY* 4.0 24.9 - - - -
18E THR* 4.3 6.1 - - + -
20E VAL* 4.0 19.5 - - + -
41E SER* 4.3 4.7 - - - +
42E PHE* 1.3 78.9 - - - +
44E ASP* 1.3 59.1 + - - +
45E ASP* 3.6 8.3 + - - +
50E LYS 4.6 0.7 - - - +
51E LYS* 3.9 1.1 - - - -
52E LEU* 2.8 44.3 + - + +
54E VAL* 4.2 10.5 - - + -
289E GLU* 4.7 0.2 - - - -
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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