Contacts of the strand formed by residues 36 - 41 (chain E) in PDB entry 4IGM
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 GLU 36 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E HIS* 4.1 4.0 + - - +
32E HIS* 3.7 28.2 + - + +
33E SER* 3.8 22.8 + - - +
34E LYS 3.1 10.4 + - - +
35E GLY* 1.3 89.3 - - - +
37E ALA* 1.3 62.2 + - - +
48E VAL* 4.4 16.2 - - + -
49E VAL 3.5 10.5 - - - +
50E ARG* 2.9 44.4 + - + +
54E TRP* 4.9 1.7 - - - -
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Residues in contact with ALA 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E LEU* 3.8 23.6 - - + -
30E GLN 3.5 10.5 - - - +
31E HIS* 4.1 16.4 - - - +
32E HIS* 4.1 3.5 - - - -
36E GLU* 1.3 76.9 - - - +
38E LYS* 1.3 62.6 + - - +
48E VAL* 3.4 6.1 - - - +
49E VAL* 2.7 43.8 + - + +
54E TRP* 4.2 9.4 - - - +
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Residues in contact with LYS 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E LEU* 3.6 3.8 - - - -
30E GLN* 2.9 37.4 + - + +
32E HIS* 3.4 38.0 + - + +
37E ALA* 1.3 73.8 - - - +
39E LEU* 1.3 63.5 + - - +
40E LEU* 3.2 13.6 - - + +
45E VAL* 4.1 32.7 - - + +
47E ARG 3.4 4.9 - - - +
48E VAL* 4.2 19.3 - - + -
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Residues in contact with LEU 39 (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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10E LEU* 3.7 22.7 - - + -
14E TRP* 4.3 3.8 - - + -
27E VAL* 3.9 22.7 - - + -
28E GLN 3.5 4.0 - - - +
29E LEU* 3.5 26.4 - - + +
37E ALA 4.3 0.4 + - - -
38E LYS* 1.3 72.9 - - - +
40E LEU* 1.3 60.0 + - - +
45E VAL* 3.7 4.2 - - - +
46E PHE* 2.9 60.0 + - + -
47E ARG* 2.8 31.2 + - + +
49E VAL* 4.8 7.0 - - + -
76E VAL* 4.8 7.6 - - + -
78E VAL* 4.5 8.1 - - + -
294E PHE* 6.1 0.4 - - + -
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Residues in contact with LEU 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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26E TRP 3.7 0.9 - - - +
27E VAL* 3.3 12.8 - - - +
28E GLN* 3.0 40.8 + - + +
30E GLN* 2.9 41.7 - - + +
38E LYS* 3.2 22.9 - - + +
39E LEU* 1.3 77.8 - - - +
41E LYS* 1.3 59.2 + - - +
42E ASP 3.9 1.0 + - - +
43E GLY* 4.1 31.2 - - - +
44E LYS 3.3 9.4 - - - +
45E VAL* 4.9 9.2 - - + +
46E PHE* 4.7 2.7 - - - -
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Residues in contact with LYS 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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25E GLY* 4.4 30.3 - - - +
26E TRP 4.0 5.2 - - - +
27E VAL* 5.7 2.5 - - + -
40E LEU* 1.3 70.7 - - - +
42E ASP* 1.3 75.2 + - + +
43E GLY 3.3 0.4 - - - -
44E LYS* 2.7 30.8 + - + +
46E PHE* 4.6 10.4 - - + +
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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