Contacts of the strand formed by residues 128 - 133 (chain B) 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 GLU 128 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127B ILE* 1.3 84.5 - - - +
129B VAL* 1.3 63.8 + - - +
130B ARG* 2.5 44.5 + - - +
174B GLN 3.5 1.6 - - - +
175B VAL* 3.2 6.8 - - - +
176B GLU* 2.9 50.7 + - + +
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Residues in contact with VAL 129 (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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117B CYS* 4.2 3.6 - - - -
119B VAL* 4.1 17.0 - - + -
127B ILE* 4.7 13.0 - - + -
128B GLU* 1.3 80.1 - - - +
130B ARG* 1.3 65.2 + - - +
157B THR* 4.7 7.9 - - + -
159B VAL* 3.6 46.3 - - + +
173B CYS* 3.5 32.1 - - - -
174B GLN 3.3 4.0 - - - +
175B VAL* 4.3 6.3 - - + -
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Residues in contact with ARG 130 (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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128B GLU* 2.5 45.2 + - - +
129B VAL* 1.3 80.7 + - - +
131B TRP* 1.3 64.1 + - - +
132B PHE* 3.6 17.9 - - + -
137B GLU* 3.3 34.0 + - - +
138B GLU 5.7 0.2 - - - -
139B LYS* 5.8 2.6 - - - +
172B THR 3.5 2.6 - - - +
173B CYS* 3.5 4.7 - - - -
174B GLN* 2.9 56.6 + - + +
176B GLU* 3.0 17.4 + - - -
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Residues in contact with TRP 131 (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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101B VAL* 4.0 24.0 - - + -
115B LEU* 3.7 36.1 - - + -
117B CYS* 3.7 23.7 - - + +
130B ARG* 1.3 76.6 - - - +
132B PHE* 1.3 58.9 + - - +
137B GLU* 3.5 5.0 - - - +
138B GLU* 2.6 48.5 + - + +
142B VAL* 3.9 17.0 - - + +
159B VAL* 3.1 32.7 + - + +
160B MET 3.7 1.3 - - - -
161B LEU* 3.6 43.8 - - + +
171B TYR* 3.8 24.0 - - + -
172B THR* 3.4 29.6 - - - -
173B CYS* 4.1 3.1 - - + -
186B VAL 5.5 0.2 - - - -
188B TRP* 5.7 0.7 - - + -
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Residues in contact with PHE 132 (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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130B ARG* 3.6 34.1 - - + -
131B TRP* 1.3 76.7 - - - +
133B ARG* 1.3 60.7 + - - +
134B ASN 3.8 0.7 + - - -
135B GLY* 3.8 24.9 - - - +
136B GLN 3.4 3.6 - - - +
137B GLU* 3.7 34.5 - - + -
138B GLU* 4.8 1.1 - - - -
161B LEU* 5.6 0.2 - - - -
170B VAL 3.9 0.2 - - - +
171B TYR* 3.1 9.5 - - - +
172B THR* 2.8 59.6 + - + +
174B GLN* 3.6 39.0 - - + -
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Residues in contact with ARG 133 (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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132B PHE* 1.3 73.0 - - - +
134B ASN* 1.3 79.6 + - - +
136B GLN* 2.8 25.6 + - + +
138B GLU* 2.9 38.6 + - + +
163B THR* 5.6 6.7 - - - +
166B ARG* 4.8 9.3 - - - +
169B GLU* 3.4 33.3 + - + +
170B VAL 4.2 1.1 - - - +
171B TYR* 3.2 32.6 + - + -
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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