Contacts of the strand formed by residues 34 - 43 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A THR 3.8 0.3 - - - +
28A TYR* 3.2 7.5 - - - -
29A ASP* 2.9 40.1 + - + -
32A ASN* 3.4 24.0 - - + +
33A GLY* 1.3 77.9 - - - +
35A HIS* 1.3 61.5 + - - +
36A LYS* 3.6 14.2 + - + +
60A THR 3.8 4.0 - - - +
61A ILE* 3.9 20.4 - - + -
249A TYR* 3.6 29.2 - - - +
250A GLU 3.8 4.0 - - - -
251A ARG* 3.8 22.7 - - + +
276A ASP* 3.6 26.0 - - + +
278A SER* 3.6 19.7 - - - -
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Residues in contact with HIS 35 (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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26A VAL* 3.6 15.8 - - + +
27A THR 3.9 1.6 - - - -
28A TYR* 3.7 6.8 - + + -
34A MET* 1.3 70.7 - - - +
36A LYS* 1.3 60.4 + - - +
37A LYS* 4.6 3.8 - - + -
58A LYS 4.1 1.2 - - - +
59A GLY* 3.3 13.3 - - - -
60A THR 2.9 38.7 + - - +
249A TYR* 4.1 2.3 - - - -
98G ILE 2.9 26.7 + - - -
99G SER* 3.7 14.4 - - - -
101G TYR* 2.7 41.0 + + - +
160G PRO* 3.5 21.1 + - + +
161G THR 3.4 26.4 + - - -
162G ASP* 3.7 6.3 - - + -
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Residues in contact with LYS 36 (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 LEU 3.7 1.0 - - - +
26A VAL* 3.4 4.8 - - - +
27A THR* 2.8 54.7 + - - +
29A ASP* 4.7 6.3 - - - +
34A MET* 3.9 12.8 - - + +
35A HIS* 1.3 77.0 - - - +
37A LYS* 1.3 60.1 + - - +
38A VAL* 6.5 0.2 - - + -
247A VAL* 4.8 2.3 + - + -
249A TYR* 3.6 47.6 - - + -
278A SER* 2.7 41.6 + - - +
279A SER 4.1 1.8 + - - -
280A GLU* 3.7 35.1 + - - +
282A TYR* 5.2 7.1 + - - +
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Residues in contact with LYS 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ASP* 2.7 25.4 + - - +
25A LEU 3.3 3.8 - - - +
26A VAL* 3.6 20.6 - - + -
35A HIS* 4.1 3.1 + - + -
36A LYS* 1.3 75.9 - - - +
38A VAL* 1.3 82.1 + - - +
39A PHE* 3.7 10.1 - - + +
56A ARG 3.6 0.5 - - - +
57A THR* 3.7 1.2 - - - -
58A LYS* 2.9 62.6 + - + -
59A GLY* 4.2 12.3 - - - +
249A TYR* 3.7 5.4 + - - -
6F ASN* 4.9 2.2 + - - -
99G SER* 2.8 40.9 + - - +
100G ASP* 3.9 12.9 + - - +
231G VAL* 5.3 0.2 - - - +
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Residues in contact with VAL 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLY 3.7 1.0 - - - +
24A ASP* 3.4 3.8 - - - -
25A LEU* 2.9 43.8 + - + +
36A LYS* 5.8 0.4 - - + -
37A LYS* 1.3 80.8 - - - +
39A PHE* 1.3 67.2 + - - +
40A TYR* 4.3 5.6 - - + +
55A ILE* 3.9 27.4 - - + -
56A ARG 3.4 4.5 - - - +
57A THR* 4.8 8.7 - - + -
247A VAL* 5.0 5.4 - - + -
249A TYR* 5.7 1.1 - - + +
282A TYR* 3.6 35.7 - - + +
291A MET* 4.2 21.5 - - + -
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Residues in contact with PHE 39 (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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22A THR* 4.2 8.7 - - - -
23A GLY 3.3 9.2 - - - -
24A ASP* 3.7 17.0 - - - -
37A LYS* 3.7 17.8 - - + +
38A VAL* 1.3 75.0 - - - +
40A TYR* 1.3 58.5 + - - +
41A SER* 3.5 9.2 - - - -
54A VAL 3.7 1.6 - - - +
56A ARG* 2.8 47.9 + - + +
58A LYS* 4.9 0.7 - - + -
6F ASN* 3.8 35.9 - - + +
12G THR* 3.4 41.7 - - + -
14G ILE* 3.2 34.1 - - + -
48G HIS* 3.6 8.1 - + - -
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Residues in contact with TYR 40 (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 LYS 4.3 1.3 - - - -
22A THR* 3.2 11.9 + - - -
23A GLY* 2.9 59.6 + - - +
24A ASP 4.1 0.2 - - - -
25A LEU* 4.2 10.3 - - + -
38A VAL* 4.4 6.3 - - + -
39A PHE* 1.3 75.3 - - - +
41A SER* 1.3 68.5 + - - +
42A PHE* 3.5 35.9 - + - -
53A LEU* 4.0 4.0 - - + -
54A VAL 3.2 9.2 - - - +
55A ILE* 4.8 1.6 - - - -
289A GLU 4.4 2.8 + - - -
290A GLU* 3.7 11.5 - - - +
291A MET* 3.3 62.5 + - + -
49G ASN* 3.7 24.0 + - - +
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Residues in contact with SER 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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20A VAL* 4.1 7.4 - - - -
21A LYS 3.4 6.3 - - - -
22A THR* 3.4 14.9 - - - +
39A PHE* 3.5 2.9 - - - -
40A TYR* 1.3 81.4 + - - +
42A PHE* 1.3 60.6 + - - +
43A ILE* 3.7 4.0 + - - +
53A LEU* 3.4 5.5 - - - +
54A VAL* 2.9 42.8 + - - +
56A ARG* 4.4 0.5 + - - -
12G THR* 3.3 39.9 - - - +
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Residues in contact with PHE 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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19A THR 4.4 0.7 - - - +
20A VAL* 3.4 9.7 - - - +
21A LYS* 2.8 31.3 + - + +
40A TYR* 3.5 30.5 - + - -
41A SER* 1.3 71.0 - - - +
43A ILE* 1.3 60.4 + - - +
44A ASP 4.0 1.5 + - - -
52A LEU 3.5 2.9 - - - -
53A LEU* 3.7 15.7 - - + -
284A ILE* 3.8 25.1 - - + -
285A ASP 3.7 13.7 - - - -
286A TRP* 3.9 24.9 - + - -
289A GLU* 3.3 45.4 - - + +
290A GLU* 3.3 36.3 - - - -
291A MET* 4.0 1.8 - - + -
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Residues in contact with ILE 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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14A ILE* 4.2 13.6 - - + +
15A GLY* 4.0 25.4 - - - -
18A THR* 4.3 10.8 - - + -
20A VAL* 4.1 19.1 - - + -
41A SER* 4.2 5.2 - - - +
42A PHE* 1.3 77.2 - - - +
44A ASP* 1.3 59.8 + - - +
45A ASP* 3.5 5.3 + - + +
48A HIS* 6.0 0.2 - - - -
50A LYS 4.7 0.5 - - - +
51A LYS 4.0 0.5 - - - -
52A LEU* 2.8 45.6 + - + +
54A VAL* 4.2 10.8 - - + -
289A GLU* 4.8 0.2 - - - -
7G ILE* 3.6 44.0 - - + -
11G THR* 4.1 7.0 - - + -
12G THR* 4.4 6.7 - - - +
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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