Contacts of the helix formed by residues 87 - 95 (chain F) in PDB entry 6D84
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 ALA 87 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55F VAL* 5.2 5.4 - - + -
58F MET* 5.7 2.5 - - + -
73F LEU* 5.0 14.6 - - + -
84F ALA* 4.1 10.8 - - - +
85F ILE 3.1 2.0 + - - -
86F MET* 1.3 79.4 - - - +
88F VAL* 1.3 61.6 + - + +
89F ASN 3.4 2.2 - - - -
90F THR* 2.4 30.8 + - - +
91F PHE* 2.9 38.5 + - + -
118F ILE* 6.5 0.4 - - + -
50I GLY* 4.5 0.2 - - - -
51I PHE* 5.9 0.2 - - + -
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Residues in contact with VAL 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84F ALA 4.8 0.9 - - - +
85F ILE* 3.8 16.6 + - + +
87F ALA* 1.3 75.6 - - + +
89F ASN* 1.3 61.4 + - - +
91F PHE* 3.2 9.4 + - + +
92F VAL* 2.9 36.4 + - + +
118F ILE* 4.1 33.4 - - + +
121F TYR* 3.8 32.1 - - + +
122F LEU* 4.1 12.3 - - + -
49I ILE* 3.8 24.5 - - + -
50I GLY* 4.0 0.2 - - - -
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Residues in contact with ASN 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87F ALA 3.4 0.4 - - - -
88F VAL* 1.3 77.7 - - - +
90F THR* 1.3 58.8 + - - +
92F VAL* 3.2 8.6 - - - +
93F LYS* 2.9 30.3 + - - +
45I THR* 5.7 1.4 - - - +
46I ILE* 3.7 18.5 - - - +
48I THR* 3.3 25.4 - - - +
49I ILE* 4.1 3.7 - - - +
50I GLY* 3.3 21.3 - - - +
51I PHE 3.1 18.4 + - - +
52I ASN* 2.7 35.6 + - - -
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Residues in contact with THR 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58F MET* 3.4 29.2 - - - +
59F GLN* 3.8 15.3 - - + +
87F ALA* 2.4 32.4 + - - +
89F ASN* 1.3 74.0 - - - +
91F PHE* 1.3 58.9 + - - +
93F LYS* 3.4 2.7 + - - +
94F ASP* 2.9 35.9 + - - +
51I PHE* 3.6 54.3 - - + +
52I ASN* 5.4 1.8 - - - +
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Residues in contact with PHE 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58F MET* 4.7 3.4 - - + -
70F TYR* 3.9 17.9 - + - -
73F LEU* 4.2 12.1 - - + -
87F ALA* 2.9 43.5 + - + -
88F VAL* 3.2 11.6 + - + +
90F THR* 1.3 78.0 + - - +
92F VAL* 1.3 58.4 + - + +
94F ASP* 3.2 3.4 + - - +
95F CYS* 2.9 35.5 + - - -
106F ALA* 3.9 13.5 - - + -
109F THR* 3.6 36.3 - - + -
110F MET* 3.6 34.5 - - + -
113F ILE* 3.7 20.4 - - + -
118F ILE* 5.8 5.4 - - + -
122F LEU* 5.5 5.6 - - + -
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Residues in contact with VAL 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88F VAL* 2.9 29.4 + - + +
89F ASN* 3.2 27.1 - - - +
91F PHE* 1.3 78.2 - - + +
93F LYS* 1.3 58.2 + - - +
95F CYS* 4.1 7.1 + - - +
96F GLU* 3.2 31.8 - - - +
110F MET* 5.6 0.7 - - + -
121F TYR 4.9 3.4 - - - +
122F LEU* 6.3 0.4 - - + -
125F PRO* 3.7 33.8 - - + +
46I ILE* 4.1 23.3 - - + -
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Residues in contact with LYS 93 (chain F).
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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59F GLN* 4.2 15.7 - - - +
89F ASN* 2.9 21.3 + - - +
90F THR* 3.6 8.1 - - - +
92F VAL* 1.3 78.3 - - - +
94F ASP* 1.3 60.2 - - - +
95F CYS 3.2 0.4 - - - -
96F GLU* 2.9 44.7 + - + +
97F ASP* 4.9 1.0 - - - +
35I TYR* 3.3 42.5 + - + +
43I VAL* 5.3 7.7 - - - +
44I THR 5.5 4.2 + - - -
45I THR* 5.8 2.2 + - - +
52I ASN* 4.4 8.1 - - - +
54I GLU* 6.1 1.3 - - - +
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Residues in contact with ASP 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58F MET* 3.3 14.0 - - - +
59F GLN* 2.9 28.3 + - - +
66F LYS* 3.5 9.9 + - - -
70F TYR* 3.3 18.2 + - - +
90F THR 2.9 20.8 + - - +
91F PHE* 4.0 3.1 - - - +
93F LYS* 1.3 74.4 - - - +
95F CYS* 1.3 57.5 + - - +
96F GLU 3.1 5.9 + - - -
97F ASP* 3.7 13.8 - - - +
102F ILE* 4.2 12.8 - - + +
103F ARG* 3.4 26.0 + - - +
106F ALA* 4.1 15.9 - - + -
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Residues in contact with CYS 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F PHE 2.9 24.0 + - - +
92F VAL 4.4 4.7 - - - +
93F LYS 3.2 0.8 - - - -
94F ASP* 1.3 74.5 - - - +
96F GLU* 1.3 61.3 + - + +
97F ASP 3.6 1.3 - - - -
103F ARG* 3.7 19.8 - - - -
106F ALA* 4.1 9.6 - - - -
107F VAL* 3.9 23.1 - - - -
110F MET* 3.8 26.5 - - - -
125F PRO* 4.5 14.6 - - + -
128F LYS* 4.3 12.4 + - + +
129F CYS* 3.9 18.4 - - - -
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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