Contacts of the helix formed by residues 42 - 51 (chain J) in PDB entry 5FLM
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 ARG 42 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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959B GLU* 4.3 22.3 + - + +
961B ILE* 3.8 25.8 - - + +
1020B TYR* 5.6 1.1 - - - -
180C ALA* 3.4 14.3 - - - +
181C GLY* 3.3 31.2 + - - +
234C GLU* 2.8 25.6 + - - -
10J CYS* 3.3 33.2 - - - +
12J LYS* 3.8 17.2 - - - +
41J LYS* 1.3 97.1 - - - +
43J TYR* 1.3 60.6 + - - +
44J CYS* 3.2 14.8 - - - -
45J CYS* 3.0 30.4 + - - +
46J ARG* 3.6 2.4 + - - +
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Residues in contact with TYR 43 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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779B ILE* 3.5 29.2 - - + +
959B GLU* 5.2 0.2 - - - -
961B ILE* 3.9 22.4 - - + +
988B LYS* 4.3 14.8 - - + +
991B ALA* 3.7 23.8 - - + +
992B ASN* 3.2 25.1 + - - +
1020B TYR* 3.3 35.9 - + - -
1026B GLU* 4.2 10.2 + - - -
1043B ILE* 3.5 26.5 - - - +
1044B GLY* 4.7 0.5 - - - -
1045B PRO* 3.9 15.3 - - + -
41J LYS 3.5 2.2 + - - -
42J ARG* 1.3 68.1 - - - +
44J CYS* 1.3 60.7 + - - +
45J CYS 3.1 0.4 - - - -
46J ARG* 3.5 13.6 - - - +
47J ARG* 2.9 31.6 + - - +
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Residues in contact with CYS 44 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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779B ILE* 4.2 8.3 - - + -
961B ILE* 3.8 16.1 - - + +
7J CYS* 3.1 14.6 - - - -
9J THR* 3.7 27.4 - - + +
10J CYS* 3.8 8.7 - - - -
42J ARG* 3.1 28.4 + - - -
43J TYR* 1.3 83.8 - - - +
45J CYS* 1.3 58.9 + - - +
47J ARG* 3.2 28.1 + - - +
48J MET* 3.8 1.2 - - - +
1068J ZN 2.6 29.4 - - - -
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Residues in contact with CYS 45 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7J CYS* 3.9 7.9 - - + -
10J CYS* 3.4 13.5 - - - -
12J LYS* 3.9 33.4 - - - -
14J VAL* 4.5 2.8 - - + +
40J LEU* 3.7 32.4 - - + +
42J ARG* 3.0 18.8 + - - +
44J CYS* 1.3 74.8 - - - +
46J ARG* 1.3 64.5 + - - +
47J ARG 3.2 0.4 - - - -
48J MET* 3.0 20.1 + - - +
49J LEU 3.8 2.3 + - - -
1068J ZN 2.6 32.6 - - - -
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Residues in contact with ARG 46 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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991B ALA 2.7 27.5 + - - +
992B ASN* 2.9 28.1 + - - +
994B GLY 3.7 7.3 - - - +
32J GLY* 3.7 21.2 + - - -
35J LEU* 3.3 45.3 - - + +
36J ASP* 3.1 28.1 + - - -
40J LEU* 3.7 24.9 + - + +
41J LYS 3.8 18.2 - - - -
42J ARG 4.1 2.2 - - - +
43J TYR* 3.0 18.9 + - - +
45J CYS* 1.3 77.7 - - - +
47J ARG* 1.3 58.2 + - - +
48J MET 3.3 0.2 + - - -
49J LEU* 3.5 1.4 + - - +
50J LEU* 2.9 32.8 + - - +
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Residues in contact with ARG 47 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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755B GLN* 4.2 7.0 + - - +
758B LEU* 3.9 22.4 - - + -
776B ILE* 4.8 1.0 - - - +
777B ASN* 2.7 37.5 + - + +
778B SER* 3.9 5.2 - - - -
779B ILE* 3.5 28.5 - - - +
964B ASP* 2.6 30.7 + - - -
991B ALA* 4.9 5.1 - - + +
1045B PRO* 4.5 10.8 - - - -
8J PHE* 4.2 4.0 - - - +
9J THR* 2.9 17.8 + - - +
43J TYR* 2.9 10.8 + - - +
44J CYS* 3.2 19.5 + - - +
46J ARG* 1.3 74.8 - - - +
48J MET* 1.3 90.7 + - + +
50J LEU* 4.0 6.5 - - - -
51J ALA* 3.2 25.6 + - + +
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Residues in contact with MET 48 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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755B GLN* 3.6 25.5 + - - +
3J ILE* 5.4 3.1 - - + +
4J PRO* 4.2 22.1 - - + +
7J CYS* 3.4 37.9 - - + -
8J PHE* 3.9 22.0 - - + -
14J VAL* 3.8 20.6 - - + -
44J CYS 3.8 1.8 - - - +
45J CYS 3.0 12.1 + - - +
47J ARG* 1.3 119.8 - - + +
49J LEU* 1.3 61.3 + - - +
52J HIS* 3.1 26.0 + - - +
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Residues in contact with LEU 49 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3J ILE* 3.5 21.5 - - + -
14J VAL* 3.6 12.8 - - + -
17J LYS* 4.0 5.2 - - + +
18J TRP* 3.4 52.3 - - + +
21J TYR* 4.0 14.8 + - + -
35J LEU* 3.5 31.6 - - + -
38J LEU* 3.6 22.9 - - + -
40J LEU* 3.6 18.8 - - + -
45J CYS 3.8 1.0 + - - -
46J ARG 3.5 2.4 + - - +
48J MET* 1.3 77.2 - - - +
50J LEU* 1.3 66.8 + - - +
52J HIS 3.4 8.1 + - - +
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Residues in contact with LEU 50 (chain J).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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756B LYS* 3.5 20.3 + - - -
758B LEU* 3.8 20.2 - - + -
990B SER 3.4 25.8 - - - +
991B ALA* 4.1 12.8 - - - +
994B GLY* 3.4 30.3 - - - +
995B GLU 4.3 4.3 - - - +
996B ILE* 4.3 16.0 - - + +
21J TYR* 4.7 5.8 - - - +
31J GLU* 4.2 17.7 - - + -
35J LEU* 4.3 7.4 - - + +
46J ARG 2.9 19.6 + - - +
47J ARG* 4.4 1.3 - - - -
49J LEU* 1.3 80.4 - - - +
51J ALA* 1.3 56.8 + - - +
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Residues in contact with ALA 51 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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755B GLN* 3.3 10.5 - - + +
756B LYS* 3.0 49.4 + - - +
757B PRO 5.3 0.4 - - - -
758B LEU* 3.7 15.9 - - + -
777B ASN* 3.4 17.9 - - - +
996B ILE* 5.6 0.7 - - - -
47J ARG 3.2 18.2 + - - +
48J MET 4.3 0.4 - - - -
50J LEU* 1.3 77.0 - - - +
52J HIS* 1.3 61.3 + - - +
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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