Contacts of the strand formed by residues 94 - 103 (chain F) in PDB entry 1E50
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 LYS 94 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87F ASP 3.8 5.5 - - - +
88F LEU* 4.1 11.0 - - - +
91F GLU* 2.9 61.4 + - + +
92F ALA 4.5 0.4 - - - +
93F GLY* 1.3 81.6 + - - +
95F VAL* 1.3 57.9 + - - +
96F TYR* 3.7 25.9 + - + -
113F TRP* 3.4 43.9 - - + +
114F ILE 3.0 23.6 - - - +
115F ASP* 3.9 6.1 - - - +
116F LEU* 3.7 9.5 - - - +
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Residues in contact with VAL 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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44F PHE* 3.8 34.3 - - + -
48F CYS* 4.5 4.5 - - + -
86F VAL* 3.8 17.7 - - + -
87F ASP 3.1 26.7 - - - +
88F LEU* 3.4 21.1 - - + +
94F LYS* 1.3 75.5 - - - +
96F TYR* 1.3 68.6 + - - +
97F LEU* 3.8 14.8 + - + +
113F TRP* 3.0 22.9 - - - -
114F ILE 3.0 7.7 + - - +
116F LEU* 4.3 3.1 - - + +
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Residues in contact with TYR 96 (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 GLU 5.2 1.0 - - - +
85F TYR 3.4 4.0 - - - +
86F VAL* 3.6 0.9 - - - -
87F ASP* 2.6 54.0 + - + +
90F ARG* 3.4 66.3 + - + +
91F GLU* 4.2 14.0 + - + -
94F LYS* 3.7 30.7 + - + -
95F VAL* 1.3 75.0 - - - +
97F LEU* 1.3 58.9 + - - +
112F GLY 3.6 6.1 - - - -
113F TRP* 3.6 37.1 + + + -
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Residues in contact with LEU 97 (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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44F PHE* 4.3 3.8 - - + -
48F CYS* 4.1 11.9 - - - -
55F ILE* 4.0 20.0 - - + -
68F PHE* 3.5 46.4 - - + -
84F GLU 5.5 0.2 - - - -
85F TYR 3.1 14.4 - - - +
86F VAL* 3.9 9.9 - - + -
95F VAL* 3.9 36.1 - - + +
96F TYR* 1.3 75.9 - - - +
98F LYS* 1.3 61.1 + - - +
110F TRP* 4.0 8.0 - - + -
111F LYS* 3.4 5.7 - - - +
112F GLY 2.7 38.5 + - - +
114F ILE* 5.1 4.3 - - + +
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Residues in contact with LYS 98 (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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68F PHE* 3.1 17.5 - - - +
84F GLU* 3.7 39.6 + - + +
85F TYR* 3.0 49.6 + - + -
97F LEU* 1.3 75.6 - - - +
99F ALA* 1.3 64.0 + - - +
100F PRO* 5.3 1.8 - - - -
109F ILE* 3.9 28.4 - - + +
110F TRP 3.3 4.0 - - - -
111F LYS* 3.2 38.4 - - + +
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Residues in contact with ALA 99 (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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66F LEU* 3.9 22.4 - - + -
67F GLN 3.5 15.7 - - - +
68F PHE* 3.8 12.8 - - + -
98F LYS* 1.3 79.8 - - - +
100F PRO* 1.3 67.1 - - - +
101F MET* 3.9 4.7 + - - +
109F ILE* 3.6 1.5 - - - -
110F TRP* 2.7 48.5 + - + +
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Residues in contact with PRO 100 (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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156E PRO* 3.2 16.2 - - + +
157E PRO* 3.6 6.6 - - - +
67F GLN 4.0 6.3 + - - +
69F PHE 3.2 26.9 - - - +
85F TYR* 4.0 12.8 - - + -
98F LYS* 5.3 2.7 - - + -
99F ALA* 1.3 84.4 - - - +
101F MET* 1.3 64.4 + - - +
108F VAL 3.6 9.0 - - - +
109F ILE* 4.3 9.4 - - + -
128F ASP* 4.4 4.0 - - - +
131F ARG* 3.4 45.5 - - - +
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Residues in contact with MET 101 (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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156E PRO* 4.0 7.1 - - - +
157E PRO* 3.5 23.8 - - + +
159E VAL* 3.8 11.9 - - + -
64F LEU* 3.5 28.9 - - + -
65F SER 5.2 1.1 - - - +
66F LEU* 4.2 21.8 - - - -
99F ALA* 3.9 8.5 + - + +
100F PRO* 1.3 74.8 - - - +
102F ILE* 1.3 70.1 + - - +
103F LEU* 3.3 40.4 - - + -
107F CYS* 3.7 3.6 - - - +
108F VAL* 3.0 45.4 + - + +
110F TRP* 4.8 4.5 - - - -
125F LEU* 5.1 0.4 - - + -
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Residues in contact with ILE 102 (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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67E SER* 5.9 1.1 - - - +
156E PRO* 4.9 9.9 - - + +
157E PRO 3.0 9.9 + - - +
158E GLN* 3.3 16.3 - - + -
159E VAL* 2.7 33.8 + - - +
2F PRO* 3.5 37.9 - - + -
3F ARG 3.5 28.3 - - - +
4F VAL* 4.0 9.6 - - + -
101F MET* 1.3 78.2 - - - +
103F LEU* 1.3 54.6 + - - +
105F GLY* 4.0 5.6 - - - +
106F VAL 3.5 20.6 - - - +
107F CYS* 3.9 13.7 - - - -
135F GLU* 4.0 9.4 - - - +
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Residues in contact with LEU 103 (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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159E VAL* 3.4 33.0 - - + +
161E THR* 4.5 2.0 - - + -
17F PHE* 3.8 26.7 - - + -
18F PHE* 3.4 11.9 - - + -
21F LEU* 5.2 0.4 - - + -
64F LEU* 4.2 11.4 - - + -
101F MET* 3.3 26.1 + - + -
102F ILE* 1.3 72.2 - - - +
104F ASN* 1.3 84.5 + - - +
105F GLY 3.2 1.3 - - - -
106F VAL 2.9 19.9 + - - +
108F VAL* 3.9 9.9 - - + -
125F LEU* 3.7 30.5 - - + -
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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