Contacts of the strand formed by residues 93 - 98 (chain D) in PDB entry 1F9N
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 MET 93 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89D SER* 3.3 5.8 - - - -
90D ALA* 2.8 48.3 + - + +
91D SER* 3.5 3.8 - - - +
92D HIS* 1.3 80.0 - - - +
94D ILE* 1.3 63.5 + - - +
95D VAL* 4.7 2.5 - - + -
129D LEU* 3.3 30.7 - - + -
130D ILE 3.2 8.3 - - - +
131D ILE* 4.4 7.0 - - + -
138D THR* 3.7 0.2 - - - +
92E HIS* 4.4 14.6 - - - -
93E MET* 4.4 9.6 - - - -
119E MET* 4.3 7.9 - - + -
131E ILE* 3.2 39.7 - - + -
93F MET* 4.0 21.5 - - + -
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Residues in contact with ILE 94 (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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87D ILE* 4.0 25.4 - - + -
88D ASP 3.4 11.7 - - - +
89D SER* 3.9 5.8 - - - +
93D MET* 1.3 72.9 - - - +
95D VAL* 1.3 65.8 + - - +
96D LEU* 3.8 1.5 + - + +
128D ILE 3.4 3.3 - - - +
129D LEU* 3.7 2.5 - - - -
130D ILE* 2.9 54.6 + - + +
132D CYS* 4.2 12.8 - - - -
138D THR* 3.4 45.3 - - + +
141D VAL* 4.2 9.2 - - + -
142D LYS* 3.8 19.3 - - + +
145D LEU* 5.0 1.3 - - + -
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Residues in contact with VAL 95 (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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86D LYS* 3.9 1.0 - - - +
87D ILE* 3.6 3.5 - - - -
88D ASP* 2.7 37.3 + - + +
93D MET* 4.7 4.9 - - + -
94D ILE* 1.3 76.8 - - - +
96D LEU* 1.3 60.7 + - - +
97D LYS* 3.8 8.7 + - + +
127D THR* 3.7 25.8 - - + -
128D ILE 3.6 3.1 - - - +
129D LEU* 4.7 2.2 - - + -
119E MET* 3.7 40.2 - - + +
120E GLY* 4.5 2.0 - - - -
131E ILE* 4.0 36.8 - - + -
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Residues in contact with LEU 96 (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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76D LEU* 6.2 0.2 - - + -
80D LEU* 4.1 23.6 - - + -
84D PHE* 3.7 28.0 - - + -
86D LYS 3.6 12.6 - - - +
87D ILE* 4.3 16.2 - - + +
94D ILE* 3.8 1.7 + - + -
95D VAL* 1.3 71.6 - - - +
97D LYS* 1.3 63.0 + - - +
98D THR* 4.1 8.9 + - + -
106D ILE* 4.2 6.3 - - + -
110D MET* 4.9 10.3 - - - -
127D THR* 3.4 1.9 - - - -
128D ILE* 2.8 67.6 + - + +
130D ILE* 4.9 11.0 - - + -
145D LEU* 5.3 8.1 - - + -
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Residues in contact with LYS 97 (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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85D VAL* 3.1 29.9 + - + -
86D LYS* 2.7 50.5 + - + +
95D VAL* 3.8 5.8 + - + +
96D LEU* 1.3 77.0 - - - +
98D THR* 1.3 68.1 + - - +
126D ASP* 3.4 7.2 - - - +
127D THR* 4.2 18.4 - - + +
111E ASP* 4.3 18.0 + - - +
119E MET 3.3 26.7 + - - -
120E GLY* 3.8 15.6 - - - -
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Residues in contact with THR 98 (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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80D LEU* 5.1 0.9 - - + -
83D ALA* 3.2 16.8 - - - +
84D PHE* 5.0 2.0 - - - -
85D VAL* 3.5 11.4 - - - +
96D LEU* 4.1 21.5 - - + +
97D LYS* 1.3 80.8 - - - +
99D MET* 1.3 73.4 + - - +
100D PRO* 4.4 0.7 - - - +
102D ASN* 3.9 0.4 - - - -
103D ALA* 3.5 18.9 + - - -
106D ILE* 3.5 29.6 - - + -
126D ASP* 2.9 27.8 + - - +
128D ILE* 4.6 6.3 - - + -
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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