Contacts of the strand formed by residues 146 - 154 (chain C) in PDB entry 1RLI
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 SER 146 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111C SER 5.3 0.2 + - - -
112C VAL 6.0 0.2 - - - -
113C LYS 3.4 11.4 + - - -
114C GLN* 3.6 4.4 - - - +
115C ALA* 2.7 33.1 + - - -
144C GLY 3.8 3.3 + - - -
145C MET* 1.3 71.4 - - - +
147C PHE* 1.3 55.9 + - - +
148C LYS* 3.2 32.3 + - - +
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Residues in contact with PHE 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A ASN* 4.0 21.3 + - - +
127A ILE* 3.3 34.8 - - + +
115C ALA 3.6 10.8 - - - -
117C VAL* 3.8 33.4 - - + -
133C ILE* 3.6 31.2 - - + -
136C PHE* 4.1 3.1 - - + -
137C GLU* 3.6 27.6 - - + +
140C PHE* 3.6 23.3 - + + -
145C MET 3.4 3.0 + - - -
146C SER* 1.3 69.9 - - - +
148C LYS* 1.3 62.2 + - - +
149C GLY 3.4 24.9 + - - -
150C TYR* 4.1 3.8 - + - -
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Residues in contact with LYS 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A ASN* 5.3 3.4 - - - +
126A LYS* 6.0 1.2 - - - +
127A ILE* 5.8 0.7 - - - -
154A GLU* 4.9 8.1 - - - +
114C GLN* 3.0 53.9 - - + +
115C ALA 2.8 10.3 + - - +
116C TYR* 3.3 30.5 - - + +
146C SER* 3.8 20.9 + - - +
147C PHE* 1.3 73.0 - - - +
149C GLY* 1.3 55.3 + - - +
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Residues in contact with GLY 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A LYS* 6.0 7.2 - - - -
127A ILE* 5.3 2.5 - - - -
166A GLN* 5.7 2.9 - - - -
116C TYR* 3.2 14.7 - - - +
117C VAL 3.2 19.2 + - - -
147C PHE* 3.4 8.7 + - - -
148C LYS* 1.3 80.4 - - - +
150C TYR* 1.3 69.4 + - - +
174C LEU* 3.9 10.5 - - - -
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Residues in contact with TYR 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A LYS* 2.6 40.4 + - + +
127A ILE* 3.3 29.6 - - + -
130A LEU* 3.5 15.6 - - + +
150A TYR* 5.2 5.7 + + - -
152A LEU* 4.3 4.3 - - - +
166A GLN* 3.6 16.9 + - - +
117C VAL* 3.0 27.6 - - + +
130C LEU* 5.2 0.4 - - + +
133C ILE* 3.8 30.1 - - + -
147C PHE* 4.1 3.1 - + + -
149C GLY* 1.3 75.3 - - - +
151C VAL* 1.3 79.2 + - - +
152C LEU* 4.3 19.7 - - + -
174C LEU* 3.7 5.9 - - - +
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Residues in contact with VAL 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A GLN* 4.4 0.2 - - - +
19C LEU* 4.3 13.2 - - + -
117C VAL* 2.9 8.1 + - - +
118C ILE* 3.6 9.8 - - + +
119C ALA* 3.0 27.2 + - - +
150C TYR* 1.3 82.6 - - - +
152C LEU* 1.3 71.8 + - - +
167C ALA* 3.9 26.5 - - - +
170C ALA* 3.9 16.2 - - + -
171C ALA* 3.9 24.0 - - + +
174C LEU* 3.9 22.4 - - + -
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Residues in contact with LEU 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A TYR* 4.5 2.7 - - - +
78C ILE* 3.9 18.4 - - + -
119C ALA* 3.4 24.9 - - + +
125C PRO* 3.5 28.0 - - + +
126C LYS* 4.1 15.6 + - + +
129C GLY 4.4 4.9 - - - +
130C LEU* 3.8 26.5 - - + -
132C LEU* 6.0 0.2 - - + -
133C ILE* 4.0 24.2 - - + -
150C TYR* 4.3 14.7 - - + -
151C VAL* 1.3 78.2 - - - +
153C GLY* 1.3 60.4 + - - +
154C GLU 4.3 0.2 + - - -
164C ASP* 4.7 1.7 - - - +
167C ALA* 4.7 3.5 - - - +
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Residues in contact with GLY 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C LEU* 4.4 2.4 - - - +
119C ALA 2.8 14.0 + - - +
120C VAL* 3.3 7.9 - - - +
121C GLY 3.0 25.6 + - - -
125C PRO* 3.3 8.2 - - - +
151C VAL* 3.9 2.0 - - - +
152C LEU* 1.3 74.5 - - - +
154C GLU* 1.3 61.1 + - - -
161C ILE* 4.0 16.8 - - - -
164C ASP* 4.0 3.6 - - - -
167C ALA* 4.1 7.6 - - - -
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Residues in contact with GLU 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C VAL* 4.3 0.2 - - - -
121C GLY 3.3 8.3 - - - +
122C GLY* 5.0 7.1 - - - +
124C ASN* 4.7 11.3 - - - +
125C PRO* 3.9 20.3 - - + +
126C LYS* 5.8 1.2 + - - +
152C LEU 4.3 0.2 + - - -
153C GLY* 1.3 72.8 - - - -
155C GLY* 1.3 60.3 + - - +
160C ASP* 4.2 3.8 - - - +
161C ILE* 3.5 20.5 - - - +
163C ARG* 6.0 1.2 + - - -
164C ASP* 3.0 25.9 + - + +
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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