Contacts of the helix formed by residues 79 - 87 (chain B) in PDB entry 5FEY
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 ASN 79 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A ASN* 5.3 0.5 - - - +
81A THR* 3.2 20.4 + - - -
34B PRO* 3.0 28.8 + - + +
36B LEU* 4.1 17.2 - - + +
42B THR* 2.8 32.1 + - + +
77B THR 3.9 0.4 + - - -
78B ASP* 1.3 70.4 - - - +
80B LEU* 1.3 62.8 + - - +
81B THR* 3.2 14.7 + - - -
82B VAL* 3.2 29.2 + - - +
83B LEU* 3.1 24.5 + - - +
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Residues in contact with LEU 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A CYS 4.6 3.1 - - - +
40A GLY* 3.6 33.5 + - - +
41A HIS* 3.6 36.8 - - + +
33B ARG* 6.1 0.2 - - - +
36B LEU* 5.1 0.6 - - - +
78B ASP* 3.2 23.3 + - + +
79B ASN* 1.3 72.9 + - - +
81B THR* 1.3 61.3 + - - +
83B LEU* 4.0 10.0 - - + +
84B LYS* 3.0 36.5 + - + +
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Residues in contact with THR 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A VAL* 3.6 36.5 - - + +
36A LEU* 5.8 0.9 - - - +
40A GLY 5.5 1.2 + - - -
42A THR* 4.4 2.4 + - - -
79A ASN* 3.1 26.2 + - - +
81A THR* 4.7 9.4 - - + -
82A VAL* 3.9 19.3 - - + +
85A ILE* 5.9 1.1 - - + -
79B ASN* 3.2 9.6 + - - -
80B LEU* 1.3 80.2 + - - +
82B VAL* 1.3 62.5 + - - +
84B LYS* 3.5 2.5 + - - +
85B ILE* 3.2 34.1 + - + +
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Residues in contact with VAL 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A THR* 3.9 15.5 - - + -
17B VAL 3.7 17.5 - - - +
18B LEU* 4.2 14.4 - - + -
27B PHE* 3.8 32.5 - - + -
34B PRO* 3.9 13.9 - - + -
79B ASN* 3.2 33.6 + - + +
81B THR* 1.3 76.2 - - - +
83B LEU* 1.3 64.3 + - - +
85B ILE* 3.1 18.0 + - - +
86B ILE* 3.1 18.2 + - + +
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Residues in contact with LEU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B THR 4.0 10.3 - - - +
29B GLU* 4.1 19.6 - - + +
33B ARG* 3.5 34.8 - - - +
34B PRO* 3.7 28.0 - - + -
78B ASP* 3.8 19.7 - - + -
79B ASN 3.1 16.4 + - - +
80B LEU* 4.0 11.2 - - + +
82B VAL* 1.3 75.8 - - - +
84B LYS* 1.3 62.6 + - + +
86B ILE* 3.5 11.0 + - + +
87B ASP* 3.1 24.6 + - - +
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Residues in contact with LYS 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ASN* 4.1 0.7 - - - +
13A ALA* 3.2 25.6 - - + +
16A GLU* 3.5 30.0 + - - -
17A VAL* 3.7 26.5 - - + -
80B LEU* 3.0 27.3 + - + +
81B THR* 3.8 4.7 - - - +
83B LEU* 1.3 77.4 - - + +
85B ILE* 1.3 63.0 + - - +
87B ASP* 3.5 17.5 + - - +
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Residues in contact with ILE 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LEU* 3.6 32.3 - - + -
10A ASN* 2.8 37.0 + - - +
13A ALA* 4.5 4.0 - - - -
14A LEU* 3.7 31.6 - - + +
17A VAL* 4.3 14.4 - - + -
81A THR* 5.6 2.5 - - + -
85A ILE* 4.2 17.7 - - + -
14B LEU* 4.5 4.3 - - + -
18B LEU* 3.8 21.8 - - + -
81B THR* 3.2 20.8 + - + +
82B VAL* 3.1 9.9 + - - +
84B LYS* 1.3 78.1 - - - +
86B ILE* 1.3 59.7 + - + +
87B ASP 3.3 0.2 - - - -
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Residues in contact with ILE 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A HIS* 2.4 48.7 + - + +
9A LEU* 5.0 1.1 - - - +
18B LEU* 3.9 30.3 - - + +
27B PHE* 3.6 37.0 - - + +
28B THR* 4.1 16.6 - - - +
29B GLU* 4.1 12.8 - - + +
82B VAL* 3.1 20.2 + - + +
83B LEU* 3.7 18.4 - - + +
85B ILE* 1.3 78.0 - - + +
87B ASP* 1.3 60.9 + - - +
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Residues in contact with ASP 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A HIS* 4.2 9.4 + - - -
10A ASN* 3.5 30.7 + - - +
29B GLU* 3.5 22.6 - - - +
83B LEU 3.1 17.3 + - - +
84B LYS* 3.6 12.8 - - - +
85B ILE 3.3 2.4 - - - -
86B ILE* 1.3 82.8 - - - +
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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