Contacts of the strand formed by residues 45 - 54 (chain D) in PDB entry 4EMG
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 MSE 45 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14D VAL* 5.2 2.7 - - + -
22D VAL* 5.2 1.3 - - - -
24D VAL* 3.8 30.3 - - + -
36D LEU* 3.8 28.3 - - + -
38D ALA 3.2 5.4 - - - +
39D TYR* 3.9 8.7 - - + -
43D LEU* 3.5 9.1 + - + +
44D ASN* 1.3 80.0 - - - +
46D VAL* 1.3 63.6 + - - +
47D LEU* 4.0 9.6 - - + -
79D PHE* 3.4 5.5 - - - -
80D VAL* 2.8 50.2 + - + +
85D VAL* 3.3 33.7 - - + -
88D ILE* 3.8 25.6 - - + -
10G PRO* 4.5 3.1 - - - -
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Residues in contact with VAL 46 (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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36D LEU* 3.9 0.2 - - - -
37D HIS* 3.0 33.3 + - + -
38D ALA* 2.9 20.7 + - + +
45D MSE 1.3 77.7 - - - +
47D LEU* 1.3 70.2 + - - +
77D MSE 3.8 29.2 - - + -
78D LEU 3.2 7.0 - - - +
79D PHE* 4.4 2.2 - - + -
9G GLU 5.0 0.9 - - - +
10G PRO* 3.4 33.2 - - + +
13G LEU* 3.9 26.2 - - + -
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Residues in contact with LEU 47 (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 VAL* 4.1 11.2 - - + -
24D VAL* 4.2 11.9 - - + -
32D LEU* 3.9 38.6 - - + -
33D ASN 4.7 0.9 - - - -
34D GLY* 4.0 23.1 - - - +
35D ARG 3.3 0.9 - - - -
36D LEU* 4.0 26.7 - - + +
45D MSE 4.0 11.4 - - + -
46D VAL* 1.3 83.0 - - - +
48D GLY* 1.3 61.0 + - - +
49D ASP 4.0 0.2 + - - -
50D ALA* 3.9 15.8 - - + +
77D MSE 3.5 2.1 - - - -
78D LEU* 2.8 43.2 + - + +
80D VAL* 4.1 7.4 - - + +
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Residues in contact with GLY 48 (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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34D GLY* 3.5 0.3 - - - -
35D ARG* 2.7 37.4 + - - +
37D HIS* 3.6 27.8 + - - -
47D LEU* 1.3 70.8 - - - +
49D ASP* 1.3 74.5 + - - +
50D ALA 3.3 2.4 + - - -
76D GLU 3.5 7.9 - - - -
77D MSE 4.0 2.0 - - - -
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Residues in contact with ASP 49 (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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33D ASN 4.0 1.2 - - - +
34D GLY* 4.0 6.2 - - - -
35D ARG* 5.6 5.2 - - + +
48D GLY* 1.3 74.9 - - - +
50D ALA* 1.3 60.7 + - - +
51D GLU* 4.0 0.5 + - - +
74D HIS* 3.5 24.6 + - - -
75D TYR 3.3 7.9 - - - -
76D GLU* 2.7 20.4 + - - +
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Residues in contact with ALA 50 (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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33D ASN 3.1 12.1 - - - +
47D LEU* 3.9 29.6 - - + +
48D GLY 4.0 0.4 - - - -
49D ASP* 1.3 74.0 - - - +
51D GLU* 1.3 61.6 + - - +
73D LYS 3.9 0.2 - - - +
74D HIS* 3.3 8.4 - - - -
75D TYR* 2.7 41.5 + - + +
78D LEU* 4.1 26.9 - - + -
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Residues in contact with GLU 51 (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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32D LEU* 3.2 8.7 - - - +
33D ASN* 2.8 47.3 + - + +
49D ASP 4.0 1.0 + - - +
50D ALA* 1.3 74.1 - - - +
52D GLU* 1.3 63.2 + - - +
53D ILE* 3.8 22.1 - - + +
72D ARG* 2.7 40.0 + - + +
73D LYS 3.4 9.4 - - - +
74D HIS* 4.5 7.4 - - + +
75D TYR* 5.4 0.2 - - - -
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Residues in contact with GLU 52 (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 ARG* 2.6 45.9 + - + -
31D GLU 3.4 4.3 - - - -
32D LEU* 3.6 18.2 - - + -
50D ALA 4.2 0.6 - - - -
51D GLU* 1.3 74.8 - - - +
53D ILE* 1.3 66.4 + - - +
54D VAL* 4.5 5.8 - - + -
71D ILE 3.8 0.9 - - - +
72D ARG* 3.3 6.6 - - - +
73D LYS* 2.8 45.2 + - + +
75D TYR* 2.8 38.6 + - + -
23G TYR* 4.5 2.7 + - - -
25G LYS* 5.1 0.7 - - - +
87G LEU* 3.9 13.9 - - - +
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Residues in contact with ILE 53 (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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29D ASP 3.6 3.3 - - - +
30D ARG* 3.7 0.2 - - - -
31D GLU* 2.9 48.6 + - + +
33D ASN* 4.0 16.2 - - - +
51D GLU* 3.8 27.8 - - + +
52D GLU* 1.3 77.5 - - - +
54D VAL* 1.3 61.9 + - - +
55D THR* 3.8 15.1 + - + +
70D THR* 3.9 21.5 - - + +
71D ILE 3.8 2.5 - - - -
72D ARG* 3.4 37.0 - - + +
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Residues in contact with VAL 54 (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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29D ASP* 3.4 13.5 - - + +
30D ARG* 3.4 36.3 - - + +
52D GLU* 3.9 10.3 - - - +
53D ILE* 1.3 74.1 - - - +
55D THR* 1.3 68.5 + - - +
70D THR* 3.1 3.6 - - - -
71D ILE* 2.8 61.6 + - + +
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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