Contacts of the strand formed by residues 119 - 126 (chain B) in PDB entry 1RPU
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 VAL 119 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A ILE* 4.2 12.8 - - + -
124A SER 3.7 1.6 - - - -
129A THR* 4.1 13.7 - - - +
132A HIS* 3.9 27.1 - - + -
133A LEU* 4.0 19.1 - - + -
136A MET* 4.3 11.2 - - + -
114B ILE 3.8 1.0 - - - +
115B ARG* 3.3 3.0 - - - -
116B PHE 3.0 30.5 + - - +
117B ARG* 3.2 11.1 + - + +
118B GLY* 1.3 82.7 - - - +
120B SER* 1.3 63.6 + - - +
121B VAL* 4.8 1.6 - - + -
144B LEU* 3.8 21.9 - - + +
147B LEU* 4.7 3.6 - - + -
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Residues in contact with SER 120 (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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122A THR 3.5 1.6 + - - +
123A ILE* 3.5 4.5 - - - -
124A SER* 2.9 39.5 + - - -
113B SER* 5.4 0.5 - - - -
114B ILE 3.3 9.6 + - - -
115B ARG* 4.2 9.4 - - - -
118B GLY 4.0 0.2 + - - -
119B VAL* 1.3 76.1 - - - +
121B VAL* 1.3 64.2 + - - +
122B THR* 4.0 8.5 + - - -
11D A 3.2 21.6 + - - -
12D C 3.5 26.2 - - - -
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Residues in contact with VAL 121 (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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121A VAL* 4.3 3.1 - - + -
122A THR 3.4 3.4 - - - +
123A ILE* 3.8 27.4 - - + -
136A MET* 3.9 19.3 - - + -
112B TYR* 3.7 1.8 - - + +
113B SER* 3.1 3.8 - - - -
114B ILE* 2.9 42.7 + - + +
119B VAL* 4.8 2.9 - - + -
120B SER* 1.3 77.0 + - - +
122B THR* 1.3 64.9 + - - +
123B ILE* 4.1 13.5 - - + -
140B SER* 3.7 27.6 - - - +
144B LEU* 4.0 19.5 - - + -
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Residues in contact with THR 122 (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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120A SER 3.5 3.6 - - - +
121A VAL* 3.6 0.7 - - - -
122A THR* 2.9 44.4 + - - -
111B THR* 3.7 8.1 - - + -
112B TYR 3.1 4.5 - - - +
113B SER* 2.8 24.8 + - - +
120B SER* 4.0 5.4 + - - -
121B VAL* 1.3 76.2 + - - +
123B ILE* 1.3 63.5 + - - +
124B SER* 3.8 11.1 + - - +
10D C 3.1 29.6 + - - +
11D A 3.8 15.0 + - - -
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Residues in contact with ILE 123 (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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119A VAL* 3.9 14.8 - - + -
120A SER 3.4 2.2 - - - -
121A VAL* 3.8 26.7 - - + -
111B THR* 3.3 5.4 - - - +
112B TYR* 2.7 44.8 + - + +
121B VAL* 4.1 5.8 - - + -
122B THR* 1.3 73.9 - - - +
124B SER* 1.3 61.4 + - - +
125B GLY 4.3 0.2 + - - -
133B LEU* 3.6 42.0 - - + +
136B MET* 4.0 7.9 - - + -
137B ALA* 3.9 22.4 - - + -
140B SER* 3.6 22.2 - - - +
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Residues in contact with SER 124 (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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118A GLY 3.8 2.1 - - - +
119A VAL* 3.8 1.0 - - - -
120A SER* 2.9 38.6 + - - -
110B CYS 3.8 5.2 - - - -
111B THR* 4.1 5.2 + - - -
122B THR* 3.8 17.7 + - - +
123B ILE* 1.3 74.9 + - - +
125B GLY* 1.3 57.5 + - - +
133B LEU* 4.0 3.6 - - - -
11C A 3.7 12.7 + - - +
12C C 2.9 37.8 + - - +
10D C 4.5 4.7 + - - -
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Residues in contact with GLY 125 (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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118A GLY 4.3 5.6 - - - -
109B GLY 3.7 0.2 - - - -
110B CYS* 2.8 37.2 + - - +
124B SER* 1.3 74.4 - - - +
126B GLY* 1.3 64.6 + - - -
129B THR* 3.7 7.9 - - - -
133B LEU* 3.6 14.8 - - - +
12C C 3.1 16.9 + - - -
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Residues in contact with GLY 126 (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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118A GLY 5.1 0.2 + - - -
107B GLN* 3.4 11.2 - - - -
108B VAL 3.7 0.4 - - - -
110B CYS* 5.0 0.2 - - - -
125B GLY* 1.3 72.9 - - - -
127B SER* 1.3 56.4 + - - -
128B ARG 2.9 3.8 - - - -
129B THR* 2.6 42.0 + - - +
130B LEU* 3.6 1.9 + - - -
13C G 3.2 36.0 + - - -
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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