Contacts of the strand formed by residues 45 - 54 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14H VAL* 5.3 2.0 - - + -
22H VAL* 5.1 1.6 - - - -
24H VAL* 3.7 30.7 - - + -
36H LEU* 3.9 27.1 - - + -
38H ALA 3.2 7.0 - - - +
39H TYR* 3.9 8.7 - - + -
43H LEU* 3.4 7.6 + - + +
44H ASN* 1.3 81.4 - - - +
46H VAL* 1.3 62.5 + - - +
47H LEU* 4.0 9.9 - - + -
78H LEU 3.6 0.2 - - - +
79H PHE* 3.4 5.9 - - - -
80H VAL* 2.8 46.6 + - + +
85H VAL* 3.4 34.1 - - + -
88H ILE* 3.9 25.8 - - + -
10M PRO* 4.6 2.5 - - - -
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Residues in contact with VAL 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36H LEU* 3.9 0.2 - - - -
37H HIS* 2.9 34.3 + - + -
38H ALA* 2.9 20.0 + - + +
45H MSE 1.3 76.5 - - - +
47H LEU* 1.3 69.9 + - - +
77H MSE 3.8 29.6 - - + -
78H LEU 3.2 7.6 - - - +
79H PHE* 4.4 2.5 - - + -
9M GLU 5.1 0.7 - - - +
10M PRO* 3.5 31.6 - - + +
13M LEU* 3.8 28.3 - - + +
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Residues in contact with LEU 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H VAL* 4.2 10.5 - - + -
24H VAL* 4.2 11.9 - - + -
32H LEU* 3.9 38.6 - - + -
33H ASN 4.6 0.9 - - - -
34H GLY* 4.0 22.4 - - - +
35H ARG 3.4 1.6 - - - -
36H LEU* 4.0 26.7 - - + -
45H MSE 4.0 11.4 - - + -
46H VAL* 1.3 82.8 - - - +
48H GLY* 1.3 60.5 + - - +
49H ASP 4.1 0.2 + - - -
50H ALA* 3.8 16.6 - - + +
77H MSE 3.5 2.4 - - - -
78H LEU* 2.8 43.5 + - + +
80H VAL* 4.2 6.5 - - + -
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Residues in contact with GLY 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34H GLY* 3.5 0.5 - - - -
35H ARG* 2.8 37.6 + - - +
37H HIS* 3.6 27.3 + - - -
47H LEU* 1.3 70.6 - - - +
49H ASP* 1.3 74.4 + - - +
50H ALA 3.3 2.6 + - - -
76H GLU 3.5 7.4 - - - -
77H MSE 3.9 2.7 - - - -
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Residues in contact with ASP 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33H ASN 3.9 4.5 - - - +
34H GLY* 4.0 2.9 - - - -
35H ARG* 4.8 4.9 + - + +
48H GLY* 1.3 74.3 - - - +
50H ALA* 1.3 60.8 + - - +
51H GLU 4.0 0.3 + - - -
74H HIS* 3.4 25.7 + - - -
75H TYR 3.3 7.0 - - - -
76H GLU* 2.7 20.7 + - - +
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Residues in contact with ALA 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32H LEU* 5.7 0.2 - - + -
33H ASN 3.1 11.7 - - - +
47H LEU* 3.8 30.7 - - + +
48H GLY 3.9 0.4 - - - -
49H ASP* 1.3 74.6 - - - +
51H GLU* 1.3 62.1 + - - +
73H LYS 3.9 0.2 - - - +
74H HIS* 3.3 7.9 - - - -
75H TYR* 2.7 42.9 + - + +
78H LEU* 4.1 25.4 - - + -
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Residues in contact with GLU 51 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32H LEU* 3.2 9.5 - - - +
33H ASN* 2.8 48.0 + - + +
49H ASP 4.0 0.6 + - - +
50H ALA* 1.3 75.1 - - - +
52H GLU* 1.3 61.8 + - - +
53H ILE* 3.8 22.1 + - + +
72H ARG* 2.7 39.3 + - + +
73H LYS 3.4 10.1 - - - +
74H HIS* 4.5 7.2 - - + +
75H TYR* 5.3 0.2 - - - -
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Residues in contact with GLU 52 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30H ARG* 2.6 47.6 + - + -
31H GLU 3.4 3.8 - - - -
32H LEU* 3.7 18.2 - - + -
50H ALA 4.2 0.4 - - - -
51H GLU* 1.3 73.9 - - - +
53H ILE* 1.3 66.2 + - - +
54H VAL* 4.0 5.1 - - + +
71H ILE 3.8 0.9 - - - +
72H ARG* 3.2 7.3 - - - +
73H LYS* 2.8 43.0 + - + +
75H TYR* 2.7 41.3 + - + -
23M TYR* 4.7 2.4 + - - -
25M LYS* 5.1 1.2 - - - +
87M LEU* 3.9 11.2 - - - +
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Residues in contact with ILE 53 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29H ASP 3.6 3.8 - - - +
30H ARG 3.8 0.3 - - - -
31H GLU* 2.9 47.7 + - + +
33H ASN* 4.0 16.2 - - - +
51H GLU* 3.8 28.0 - - + +
52H GLU* 1.3 78.3 - - - +
54H VAL* 1.3 62.0 + - - +
55H THR* 3.8 22.0 + - + +
70H THR* 3.9 15.3 - - - +
71H ILE 3.9 2.2 - - - -
72H ARG* 3.5 36.3 - - + +
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Residues in contact with VAL 54 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28H GLY 5.7 0.4 - - - +
29H ASP* 3.4 14.4 - - + +
30H ARG* 3.4 37.0 - - + +
52H GLU* 4.0 9.4 - - - +
53H ILE* 1.3 74.7 - - - +
55H THR* 1.3 69.1 + - - +
70H THR* 3.1 4.2 + - - -
71H ILE* 2.8 61.2 + - + +
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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