Contacts of the strand formed by residues 145 - 153 (chain E) in PDB entry 1R5I
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 PHE 145 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12E PHE* 3.7 26.2 - + - -
110E ASP* 3.3 0.3 - - - +
111E LYS 3.2 24.1 + - - -
112E PHE* 2.7 47.1 + - + +
113E THR* 3.8 11.0 - - - -
115E PRO* 3.4 40.4 - - + -
137E PHE* 3.8 19.5 - - + -
138E LEU 3.3 16.2 - - - +
139E PRO* 4.7 4.3 - - + -
140E ARG* 3.6 5.3 - - - +
143E HIS 4.2 2.7 - - - -
144E LEU* 1.3 77.9 - - - +
146E ARG* 1.3 62.4 + - - +
8F LEU* 4.0 6.3 - - + -
10F GLN* 3.5 33.7 - - - -
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Residues in contact with ARG 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E ASP* 5.2 1.6 + - - -
28E GLY* 2.8 35.2 + - - -
109E ILE 3.5 4.9 - - - +
110E ASP* 2.9 33.0 - - + +
112E PHE* 4.4 1.6 - - - -
137E PHE* 3.7 2.4 - - - -
138E LEU* 2.8 54.5 + - + +
139E PRO* 4.3 11.1 + - - +
140E ARG* 4.2 11.4 - - + +
145E PHE* 1.3 74.0 - - - +
147E LYS* 1.3 62.9 + - - +
148E PHE* 4.0 28.0 - - + -
149F GLN* 3.0 27.5 + - - +
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Residues in contact with LYS 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107E CYS 3.8 0.6 - - - +
108E PHE* 3.8 1.2 - - - -
109E ILE* 3.0 45.0 + - + +
112E PHE* 4.4 6.3 - - + -
117E VAL* 3.8 17.5 - - + -
134E GLU* 2.7 30.0 + - - +
135E THR* 2.9 24.3 + - - +
136E VAL* 3.7 12.3 - - - +
137E PHE* 3.5 43.5 - - + -
146E ARG* 1.3 77.3 - - - +
148E PHE* 1.3 71.6 + - - +
149E HIS* 3.2 22.1 - - + -
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Residues in contact with PHE 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106E ILE* 4.1 7.0 - - + -
107E CYS 3.5 4.3 - - - +
108E PHE* 3.6 25.4 - + + -
134E GLU* 3.2 2.8 - - - -
135E THR* 2.9 40.0 + - + +
138E LEU* 3.3 31.9 - - + -
146E ARG* 4.0 29.6 - - - -
147E LYS* 1.3 81.6 - - - +
149E HIS* 1.3 66.7 + - - +
150E TYR* 3.4 20.4 - - + +
149F GLN* 3.1 28.7 - - + -
150F ASN 3.0 21.1 - - - -
151F GLY* 3.8 10.3 - - - -
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Residues in contact with HIS 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105E LEU 3.7 0.3 - - - +
106E ILE* 3.5 4.9 - - - +
107E CYS* 2.9 44.4 + - + +
109E ILE* 4.3 5.9 - - - +
117E VAL* 5.2 0.2 - - + -
119E VAL* 3.3 49.7 + - + +
121E TRP* 3.7 19.9 - + - +
132E VAL* 6.3 1.8 - - + -
133E SER 3.5 6.5 - - - -
134E GLU* 3.6 25.5 + - + -
147E LYS* 3.2 33.3 - - + +
148E PHE* 1.3 78.7 + - - +
150E TYR* 1.3 64.2 + - - +
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Residues in contact with TYR 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E ARG* 3.5 20.0 - - - -
104E VAL* 4.2 11.4 - - + -
105E LEU 3.4 2.7 - - - +
106E ILE* 3.9 30.7 - - + -
121E TRP* 3.6 2.7 + - - -
132E VAL* 3.2 10.7 - - - +
133E SER* 2.8 59.0 + - - +
134E GLU* 4.5 1.1 - - - -
135E THR* 3.7 8.7 - - + -
148E PHE* 3.4 23.2 - - + +
149E HIS* 1.3 76.5 - - - +
151E LEU* 1.3 62.5 + - - +
152E PRO* 4.0 4.5 - - + -
150F ASN 2.5 30.1 + - - -
151F GLY* 3.1 21.1 + - - -
152F ASP* 4.4 12.3 - - + -
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Residues in contact with LEU 151 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104E VAL* 4.1 1.5 - - - +
105E LEU* 2.8 39.6 + - + +
121E TRP* 3.5 50.3 - - + +
123E ARG* 5.5 1.8 - - - +
128E VAL* 3.8 20.2 - - + -
130E THR 4.4 5.6 - - - +
132E VAL* 3.6 18.6 - - + -
150E TYR* 1.3 75.7 - - - +
152E PRO* 1.3 81.1 - - + +
153E PHE* 3.4 6.8 + - + -
161E TYR* 3.9 29.2 - - + -
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Residues in contact with PRO 152 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103E ASN 3.5 11.0 - - - +
104E VAL* 3.9 15.5 - - + -
123E ARG* 5.8 0.7 + - - -
130E THR 5.2 1.6 - - - +
131E GLY* 3.3 35.2 - - - +
133E SER* 6.0 0.4 - - - +
150E TYR* 4.0 5.2 - - + +
151E LEU* 1.3 99.2 - - + +
153E PHE* 1.3 61.4 + - - +
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Residues in contact with PHE 153 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E THR* 4.1 7.9 - - + -
97E VAL* 5.2 0.9 - - + -
102E PRO* 3.7 2.9 - - - +
103E ASN* 2.9 49.6 + - + +
104E VAL 3.6 18.4 - - - -
105E LEU* 3.6 26.2 - - + -
123E ARG* 5.4 2.9 - - - +
151E LEU* 3.6 19.1 - - + +
152E PRO* 1.3 75.0 - - - +
154E LEU* 1.3 63.3 + - - +
155E PRO* 3.5 27.4 - - + +
161E TYR* 3.8 32.3 - + + +
178E TRP* 3.9 34.8 - + - -
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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