Contacts of the strand formed by residues 123 - 130 (chain D) in PDB entry 1RRP
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 LYS 123 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49D ARG* 5.7 3.6 - - - +
115D LEU* 3.3 4.2 - - - +
116D ASP* 2.9 27.4 + - - +
119D ASP* 3.5 35.9 + - - +
121D LEU* 3.5 26.5 - - + +
122D PRO* 1.3 79.5 - - - +
124D PRO* 1.3 66.5 - - + +
125D GLU* 3.0 38.7 + - + +
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Residues in contact with PRO 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D HIS* 3.3 29.4 - - + +
114D ALA 3.6 2.7 - - - +
115D LEU* 4.0 14.8 - - + -
122D PRO 4.4 2.2 - - - +
123D LYS* 1.3 81.8 - - + +
125D GLU* 1.3 60.3 + - - +
126D GLN* 4.0 3.8 + - - +
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Residues in contact with GLU 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D ARG* 3.6 45.7 + - + +
60D ARG* 3.9 17.1 + - - -
113D HIS* 3.1 2.9 + - - -
114D ALA 3.1 28.5 + - - +
116D ASP* 3.5 25.1 - - - +
119D ASP* 4.5 2.1 - - - +
123D LYS* 3.0 44.3 + - + +
124D PRO* 1.3 75.9 - - - +
126D GLN* 1.3 60.8 + - - +
127D LEU* 3.7 14.4 + - + +
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Residues in contact with GLN 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D ARG* 3.7 0.7 - - - +
50D PHE* 3.2 40.6 + - + +
52D VAL* 4.4 19.8 - - - +
57D TRP* 3.4 7.0 - - + -
111D VAL* 5.2 6.3 - - + -
112D TRP 3.8 5.4 - - - +
113D HIS* 4.2 18.8 - - + +
124D PRO 5.0 2.2 - - - +
125D GLU* 1.3 75.8 - - - +
127D LEU* 1.3 63.8 + - - +
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Residues in contact with LEU 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D LEU* 4.4 16.8 - - + -
48D PHE 3.3 15.9 - - - +
49D ARG* 3.9 18.4 - - + -
57D TRP* 3.5 3.6 - - - -
60D ARG* 5.7 2.2 - - + +
89D CYS 5.8 0.7 - - - +
90D ALA* 5.6 0.9 - - + -
92D HIS* 3.7 21.1 - - + +
111D VAL* 2.7 39.3 - - - +
112D TRP* 2.7 52.8 + - + +
114D ALA* 4.5 2.7 - - + -
116D ASP* 4.7 10.3 - - + +
125D GLU* 4.0 17.9 - - + +
126D GLN* 1.3 79.7 - - - +
128D ALA* 1.3 59.6 + - - +
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Residues in contact with ALA 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D LEU* 3.0 6.4 - - - +
48D PHE* 2.6 57.0 + - + -
57D TRP* 3.7 19.1 - - + -
103D ASN* 6.1 4.5 - - - -
109D SER* 6.0 2.5 - - - -
110D PHE 3.0 9.9 - - - +
111D VAL* 4.5 3.6 - - + -
112D TRP* 4.0 0.7 - - - -
127D LEU* 1.3 77.6 - - - +
129D ILE* 1.3 61.2 + - - +
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Residues in contact with ILE 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D ALA* 4.0 13.9 - - + -
46D LYS 3.5 15.5 - - - +
47D LEU* 3.6 17.9 - - + -
48D PHE* 5.1 0.4 - - - -
65D VAL* 3.4 29.8 - - + -
80D MET* 3.8 7.0 - - - -
109D SER* 2.8 23.0 - - - -
110D PHE* 2.8 35.6 + - + +
112D TRP* 3.7 19.5 - - + -
128D ALA* 1.3 75.3 - - - +
130D ARG* 1.3 61.5 + - - +
131D PHE* 4.0 17.5 - - + -
140D PHE* 4.2 9.4 - - + -
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Residues in contact with ARG 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D ALA* 3.4 4.0 - - - +
46D LYS* 2.9 66.8 + - + +
48D PHE* 3.7 28.8 - - + -
106D SER* 4.9 3.4 + - - +
108D ARG* 3.6 30.5 - - + +
109D SER* 3.3 22.7 + - - +
129D ILE* 1.3 73.9 - - - +
131D PHE* 1.3 69.6 + - - +
132D LYS 4.4 0.2 + - - -
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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