Contacts of the strand formed by residues 130 - 137 (chain A) in PDB entry 1I4R
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 ASN 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A LEU 3.9 5.8 + - - -
129A GLN* 1.3 97.0 + - - +
131A VAL* 1.3 61.2 + - - +
132A LEU 4.2 0.8 + - - -
146A GLU* 3.5 35.9 + - - +
147A VAL 3.4 4.1 - - - +
148A GLN* 3.0 34.9 + - - +
225A SER 4.4 1.2 - - - +
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Residues in contact with VAL 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A GLN* 4.4 7.6 - - + +
130A ASN* 1.3 77.1 - - - +
132A LEU* 1.3 68.2 + - - +
133A ILE* 3.6 2.7 + - + +
146A GLU* 3.3 5.3 - - - -
147A VAL* 2.9 41.4 + - + +
149A THR* 4.7 1.6 - - + -
159A LEU* 4.2 19.7 - - + -
225A SER* 3.6 30.5 - - - +
228A VAL* 4.0 22.2 - - + +
230A ILE* 3.8 28.7 - - + -
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Residues in contact with LEU 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A ASN 4.2 1.0 + - - -
131A VAL* 1.3 75.6 - - - +
133A ILE* 1.3 73.5 + - - +
134A ARG* 3.8 38.5 - - + +
144A SER* 3.9 21.3 - - - -
145A PHE* 3.8 13.5 - - - +
146A GLU* 4.3 16.0 - - + +
228A VAL 5.5 1.0 + - - -
229A LYS* 4.9 2.1 - - - -
230A ILE* 3.7 22.2 + - - +
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Residues in contact with ILE 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A VAL* 3.9 10.5 - - + +
132A LEU* 1.3 76.7 - - - +
134A ARG* 1.3 65.1 + - - +
135A VAL* 3.8 0.7 + - + -
144A SER* 3.1 5.4 - - - -
145A PHE* 2.8 74.2 + - + +
147A VAL* 4.1 16.2 - - + -
159A LEU 5.1 0.4 - - - +
163A ALA* 4.4 12.6 - - + -
230A ILE* 3.5 42.6 - - + -
232A VAL* 3.8 29.6 - - + -
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Residues in contact with ARG 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A LEU* 3.8 29.6 - - + +
133A ILE* 1.3 73.0 - - - +
135A VAL* 1.3 61.8 + - - +
136A TYR* 3.8 27.3 - - + -
141A ASN* 3.7 17.9 + - - +
144A SER* 3.6 23.4 + - - +
230A ILE 3.1 13.4 + - - +
231A GLU* 3.4 8.8 - - + -
232A VAL* 2.8 26.3 + - - +
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Residues in contact with VAL 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A ILE* 4.7 0.7 - - + -
134A ARG* 1.3 74.9 - - - +
136A TYR* 1.3 65.2 + - - +
137A GLU* 4.5 5.8 - - + +
141A ASN* 2.9 21.0 + - - -
142A THR* 3.1 18.9 + - - +
143A ILE* 2.8 37.4 + - + +
145A PHE* 3.7 30.3 - - + -
167A LEU* 3.9 17.9 - - + -
171A LYS* 5.7 1.6 - - + -
232A VAL* 3.5 7.9 - - + +
234A LEU* 3.6 26.2 - - + -
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Residues in contact with TYR 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A ARG* 3.8 40.9 - - + -
135A VAL* 1.3 78.3 - - - +
137A GLU* 1.3 59.6 + - - +
138A ASN 4.1 0.2 - - - -
139A LYS* 3.9 19.1 - - - +
140A ARG 3.2 6.5 - - - +
141A ASN* 3.8 31.4 + - + +
231A GLU* 4.2 19.7 + - + -
232A VAL 2.6 15.4 + - - +
233A HIS* 3.8 34.8 - + + -
234A LEU* 2.7 37.4 + - - +
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Residues in contact with GLU 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A VAL* 4.2 9.3 + - + +
136A TYR* 1.3 77.0 - - - +
138A ASN* 1.3 78.6 + - - +
140A ARG* 2.7 26.4 + - - +
142A THR* 2.6 39.2 + - + +
171A LYS* 3.2 23.3 + - - -
181A TYR* 2.7 43.3 + - + +
234A LEU* 3.4 4.9 - - + -
236A THR* 5.3 4.5 - - + +
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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