Contacts of the strand formed by residues 36 - 41 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D HIS* 3.8 6.6 + - - -
32D HIS* 3.7 28.9 + - + -
33D SER* 3.1 32.9 + - - +
34D LYS 3.2 10.0 - - - +
35D GLY* 1.3 84.4 - - - +
37D ALA* 1.3 64.1 + - - +
48D VAL* 4.6 11.4 - - + +
49D VAL 3.6 7.0 - - - +
50D ARG* 4.2 29.6 + - + +
54D TRP* 4.9 1.7 - - - -
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Residues in contact with ALA 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D LEU* 3.8 20.6 - - + -
30D GLN 3.0 18.4 - - - +
31D HIS* 3.9 15.5 - - + +
32D HIS* 3.6 6.7 - - - -
36D GLU* 1.3 76.7 - - - +
38D LYS* 1.3 61.6 + - - +
48D VAL* 3.5 10.6 - - - +
49D VAL* 2.9 38.7 + - + +
50D ARG* 4.9 0.2 - - - +
54D TRP* 4.3 4.0 - - - +
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Residues in contact with LYS 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D GLN 3.6 1.9 - - - +
29D LEU* 3.6 4.4 - - - -
30D GLN* 2.8 40.8 + - + +
32D HIS* 3.7 34.7 - - + +
37D ALA* 1.3 78.0 - - - +
39D LEU* 1.3 59.6 + - - +
40D LEU* 3.9 14.8 + - + +
45D VAL* 4.0 25.9 - - + +
47D ARG 3.5 5.8 - - - +
48D VAL* 4.3 17.5 - - + -
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Residues in contact with LEU 39 (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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10D LEU* 3.8 24.9 - - + -
14D TRP* 4.2 3.1 - - + -
27D VAL* 3.8 22.4 - - + -
28D GLN 3.4 5.2 - - - +
29D LEU* 3.5 25.8 - - + -
38D LYS* 1.3 71.5 - - - +
40D LEU* 1.3 60.3 + - - +
45D VAL* 3.7 4.2 - - - -
46D PHE* 2.8 51.6 + - + -
47D ARG* 2.8 33.7 + - + +
49D VAL* 4.8 9.8 - - + +
76D VAL* 4.9 6.7 - - + -
78D VAL* 4.8 10.8 - - + -
294D PHE* 5.9 0.4 - - + -
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Residues in contact with LEU 40 (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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26D TRP 3.5 2.1 - - - +
27D VAL* 3.2 5.8 - - - -
28D GLN* 2.8 44.1 + - + +
30D GLN* 3.7 29.4 - - + +
38D LYS* 4.1 18.6 - - + +
39D LEU* 1.3 80.6 - - - +
41D LYS* 1.3 60.3 + - - +
42D ASP 3.9 2.0 + - - +
43D GLY 4.4 14.8 - - - +
44D LYS 3.4 10.1 - - - +
45D VAL* 3.9 26.2 - - + -
46D PHE* 5.0 0.7 - - - -
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Residues in contact with LYS 41 (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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25D GLY* 4.4 14.7 + - - +
26D TRP 3.6 13.2 - - - +
27D VAL* 4.5 7.5 - - + +
39D LEU 4.2 0.8 + - - -
40D LEU* 1.3 73.1 - - - +
42D ASP* 1.3 71.4 + - - +
44D LYS* 3.2 13.1 + - - +
46D PHE* 4.2 32.5 - - + +
78D VAL* 3.7 26.1 + - + +
83D TRP* 5.8 4.2 - - - +
176D TRP* 4.7 7.7 - - - +
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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