Contacts of the helix formed by residues 36 - 44 (chain D) in PDB entry 5FJV
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 LEU 36 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45C ASN* 4.1 23.3 - - - +
47C TRP* 3.6 34.2 + - + +
50C PRO* 3.1 40.8 - - + -
93C LYS* 3.7 18.4 - - + +
34D ASP* 2.1 31.3 + - - +
35D ARG* 1.3 67.6 - - + +
37D PHE* 1.3 61.2 + - - +
38D LYS 3.1 3.1 - - - -
39D HIS* 3.4 11.0 + - - +
40D LEU* 3.1 22.9 + - - +
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Residues in contact with PHE 37 (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 GLU* 2.9 52.5 - - + -
34D ASP 3.4 7.5 + - - +
35D ARG 3.7 0.4 - - - -
36D LEU* 1.3 79.1 - - - +
38D LYS* 1.3 52.1 + - - +
40D LEU* 3.4 32.9 - - + -
41D PHE* 2.5 55.7 + + + +
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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
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33D GLU* 3.1 19.5 + - + +
35D ARG* 4.5 8.3 - - - +
36D LEU 4.3 0.2 - - - +
37D PHE* 1.3 78.2 - - - +
39D HIS* 1.3 68.0 + - - +
40D LEU 3.2 0.2 - - - -
41D PHE* 3.3 10.7 + - + +
42D ARG* 3.3 25.7 + - - +
96D TRP* 2.8 62.3 - - + +
101D PHE* 3.0 52.5 - - + -
105D THR 3.4 1.4 + - - -
106D SER* 4.6 1.2 - - - +
107D LEU* 3.8 26.4 - - + +
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Residues in contact with HIS 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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47C TRP* 4.9 19.3 - + + -
49C ARG* 3.4 30.5 + - + +
50C PRO* 3.8 35.6 - - + +
35D ARG 3.9 13.9 + - - -
36D LEU* 3.4 12.1 + - - +
38D LYS* 1.3 78.8 - - - +
40D LEU* 1.3 55.7 + - - +
42D ARG* 3.9 6.1 - - - +
43D GLY* 2.8 34.0 + - - -
107D LEU* 4.5 17.8 - - + +
108D ARG 4.8 3.7 + - - -
109D VAL* 4.4 22.8 - - + +
110D PRO* 5.0 2.8 - - + +
113D MET* 5.6 4.3 - - + -
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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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47C TRP* 5.0 21.8 - - + +
36D LEU 3.1 15.1 + - - +
37D PHE* 3.5 38.6 - - + +
39D HIS* 1.3 81.1 - - - +
41D PHE* 1.3 63.9 + - - +
43D GLY 4.7 0.4 - - - +
44D TYR* 3.1 42.9 + - + +
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Residues in contact with PHE 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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33D GLU* 4.7 7.4 - - - +
37D PHE* 2.5 43.4 + + + +
38D LYS* 3.8 8.3 - - + +
39D HIS 3.2 0.6 - - - -
40D LEU* 1.3 81.5 - - - +
42D ARG* 1.3 74.5 + - + +
44D TYR* 4.2 8.1 - - - +
45D ASN* 4.4 10.7 + - - +
95D ARG 4.6 11.0 - - - -
96D TRP* 5.1 10.1 - - + -
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Residues in contact with ARG 42 (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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38D LYS* 3.3 21.9 + - - +
39D HIS* 4.2 3.8 - - - +
41D PHE* 1.3 92.7 - - + +
43D GLY* 1.3 63.6 + - - +
44D TYR 3.2 2.0 - - - -
45D ASN* 3.3 10.4 - - - +
46D ARG* 3.3 19.8 - - - +
93D LYS 4.3 9.9 - - - +
94D LEU* 3.2 45.7 - - + +
95D ARG 3.9 9.2 - - - +
96D TRP* 3.5 20.5 - - - -
107D LEU* 3.9 29.3 - - - +
109D VAL* 4.3 5.7 - - - +
139D LEU* 3.0 36.4 - - - +
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Residues in contact with GLY 43 (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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39D HIS 2.8 20.0 + - - -
40D LEU* 5.2 0.7 - - - -
42D ARG* 1.3 74.8 - - - +
44D TYR* 1.3 64.2 + - - +
45D ASN 3.6 0.5 + - - -
46D ARG* 3.6 18.8 + - - +
113D MET* 6.3 4.9 - - - -
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Residues in contact with TYR 44 (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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40D LEU* 3.1 35.4 + - + +
41D PHE* 4.2 7.6 - - - +
42D ARG 3.2 0.8 - - - -
43D GLY* 1.3 78.2 - - - +
45D ASN* 1.3 63.8 + - + +
46D ARG 4.9 0.5 - - - +
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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