Contacts of the strand formed by residues 146 - 154 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111B SER 4.9 2.1 + - - -
113B LYS 3.4 11.0 + - - -
114B GLN* 3.6 6.5 - - - +
115B ALA* 2.8 28.2 + - - +
144B GLY 3.9 2.1 + - - -
145B MET* 1.3 72.2 - - - +
147B PHE* 1.3 59.9 + - - +
148B LYS* 3.2 24.3 + - - -
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Residues in contact with PHE 147 (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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115B ALA 3.6 10.8 - - - -
117B VAL* 3.8 24.7 - - + -
133B ILE* 3.6 27.4 - - + -
136B PHE* 4.1 2.5 - - + -
137B GLU* 3.7 29.2 - - + +
140B PHE* 3.6 31.4 - + + -
145B MET 3.5 4.2 + - - -
146B SER* 1.3 67.3 - - - +
148B LYS* 1.3 60.2 + - - +
149B GLY* 3.3 24.4 + - - -
150B TYR* 4.0 17.0 - + + -
124D ASN* 5.6 2.4 + - - -
126D LYS* 4.0 9.9 - - - +
127D ILE* 3.8 27.7 - - + +
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Residues in contact with LYS 148 (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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114B GLN* 3.6 45.4 - - + +
115B ALA 2.9 8.2 + - - +
116B TYR* 3.3 32.8 - - + +
146B SER* 3.8 22.4 - - - +
147B PHE* 1.3 73.5 - - - +
149B GLY* 1.3 56.6 + - - +
126D LYS* 3.6 11.1 - - - +
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Residues in contact with GLY 149 (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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115B ALA 3.9 0.2 + - - -
116B TYR* 3.2 21.9 - - - +
117B VAL 3.1 19.8 + - - -
147B PHE* 3.3 8.7 + - - -
148B LYS* 1.3 80.6 - - - +
150B TYR* 1.3 64.1 + - - +
174B LEU* 4.1 6.7 - - - -
126D LYS* 3.5 14.8 - - - +
166D GLN* 6.1 1.1 - - - -
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Residues in contact with TYR 150 (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 VAL* 3.0 26.2 - - + +
130B LEU* 5.0 3.6 - - + -
133B ILE* 3.8 44.4 - - + -
147B PHE* 4.0 10.1 - + + -
149B GLY* 1.3 77.6 - - - +
151B VAL* 1.3 74.4 + - - +
152B LEU* 4.5 13.7 - - + -
170B ALA* 5.6 0.3 - - - +
174B LEU* 4.0 5.8 - - - +
126D LYS* 2.6 66.3 + - + +
127D ILE* 4.1 3.6 - - + -
130D LEU* 3.6 12.7 - - + +
150D TYR* 5.0 7.0 + + - -
152D LEU* 4.3 4.7 - - - +
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Residues in contact with VAL 151 (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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19B LEU* 3.9 18.3 - - + +
117B VAL* 2.9 8.3 + - - +
118B ILE* 3.4 8.0 - - + +
119B ALA* 3.0 25.1 + - - +
150B TYR* 1.3 81.4 - - - +
152B LEU* 1.3 74.8 + - - +
167B ALA* 3.7 24.2 - - - +
170B ALA* 3.9 17.9 - - + -
171B ALA* 3.8 25.4 - - + +
174B LEU* 4.0 18.2 - - + -
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Residues in contact with LEU 152 (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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78B ILE* 4.0 14.6 - - + -
119B ALA* 3.3 25.8 - - + +
125B PRO* 3.7 17.0 - - + +
126B LYS* 3.5 40.0 - - + +
129B GLY 4.3 7.4 - - - +
130B LEU* 3.8 27.8 - - + -
132B LEU* 5.4 2.2 - - + -
133B ILE* 3.8 28.5 - - + -
150B TYR* 4.5 10.4 - - + -
151B VAL* 1.3 83.2 - - - +
153B GLY* 1.3 58.3 + - - +
167B ALA* 4.0 1.9 - - - +
150D TYR* 4.5 2.2 - - - +
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Residues in contact with GLY 153 (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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19B LEU* 4.2 5.5 - - - +
119B ALA 2.8 11.0 + - - -
120B VAL* 3.2 6.3 - - - -
121B GLY 3.1 23.4 + - - -
125B PRO* 3.1 10.0 - - - +
126B LYS* 4.3 0.9 - - - -
151B VAL 4.0 0.4 - - - -
152B LEU* 1.3 75.5 - - - +
154B GLU* 1.3 60.7 + - - -
161B ILE* 3.8 7.4 - - - -
164B ASP* 3.7 8.1 - - - -
167B ALA* 3.8 10.8 - - - -
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Residues in contact with GLU 154 (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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120B VAL* 4.0 2.7 - - - -
121B GLY 3.4 9.0 - - - +
122B GLY* 4.5 12.4 - - - +
124B ASN* 4.6 9.9 + - - +
125B PRO* 3.8 18.2 - - + +
126B LYS* 4.7 10.8 + - - +
153B GLY* 1.3 73.7 - - - -
155B GLY* 1.3 60.5 - - - +
156B ASN* 5.5 4.9 + - - +
160B ASP 4.2 2.9 - - - +
161B ILE* 3.5 18.8 - - - +
164B ASP* 2.8 23.5 + - - +
176D LYS* 3.7 26.4 + - - -
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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