Contacts of the strand formed by residues 77 - 82 (chain B) 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 ARG 77 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181A ALA* 2.6 39.4 + - - +
182A LEU 3.0 7.9 + - - -
183A ALA* 4.2 1.7 - - - +
184A PRO* 3.7 11.1 - - - +
33B GLY 3.1 22.2 + - - -
37B GLU* 3.1 34.2 + - - +
67B ILE* 3.5 8.7 - - - +
68B LEU* 2.7 39.7 + - + +
75B LYS 3.6 0.6 + - - +
76B ILE* 1.3 74.9 - - - +
78B LEU* 1.3 61.8 + - - +
79B LEU* 4.3 14.0 - - - +
91B ASN* 2.9 32.9 - - - +
92B HIS 3.3 13.5 - - - +
93B TYR* 3.8 18.8 - - + +
94B ILE* 4.0 4.9 - - - +
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Residues in contact with LEU 78 (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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65B VAL* 4.7 11.4 - - + -
66B LYS 3.5 13.0 - - - +
67B ILE* 4.8 1.6 - - + +
77B ARG* 1.3 73.2 - - - +
79B LEU* 1.3 64.0 + - - +
80B MET* 4.4 4.9 - - + +
90B ALA* 3.9 19.2 - - + +
91B ASN* 3.4 24.7 + - - -
92B HIS* 2.8 35.6 + - + +
94B ILE* 4.1 9.4 - - + +
112B TRP* 4.3 13.0 - - + -
140B PHE* 3.8 23.8 - - + -
144B PHE* 3.7 28.0 - - + -
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Residues in contact with LEU 79 (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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181A ALA* 3.3 29.4 - - + -
34B GLU* 3.1 35.0 - - - +
64B ASN 3.6 1.6 - - - +
66B LYS* 2.9 41.2 + - + +
68B LEU* 4.3 14.3 - - + +
77B ARG* 3.9 14.6 - - - +
78B LEU* 1.3 73.4 - - - +
80B MET* 1.3 64.6 + - - +
81B ARG* 3.9 7.0 - - + +
88B ILE* 3.6 12.8 - - + -
90B ALA 3.5 14.6 - - - +
91B ASN* 3.5 21.8 - - - +
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Residues in contact with MET 80 (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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45B ALA 3.0 35.2 - - - +
47B LEU* 3.6 28.0 - - - +
61B GLY 4.0 13.0 - - - +
62B ILE 4.4 0.2 - - - -
63B GLY 3.7 18.2 - - - +
64B ASN 3.5 6.5 - - - +
65B VAL* 3.1 33.4 - - + -
78B LEU* 4.6 0.9 - - + -
79B LEU* 1.3 76.4 - - - +
81B ARG* 1.3 66.2 + - - +
88B ILE* 3.3 9.2 - - - +
89B CYS* 2.8 33.4 + - - -
90B ALA* 3.1 24.5 + - + +
129B ILE* 3.9 1.6 - - + -
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Residues in contact with ARG 81 (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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178A ALA* 3.3 10.1 - - - +
179A MET* 2.6 56.8 + - - +
181A ALA* 3.5 18.8 - - - +
32B THR* 3.9 6.7 + - - -
34B GLU* 3.3 26.3 + - - +
62B ILE 3.8 0.5 - - - +
63B GLY* 3.3 23.7 + - - -
64B ASN* 3.5 11.6 + - + +
66B LYS* 5.6 3.3 - - - +
79B LEU* 3.9 5.9 - - + +
80B MET* 1.3 80.0 - - - +
82B ARG* 1.3 67.5 + - - +
86B LEU* 3.7 27.1 - - + -
87B LYS 3.3 23.6 - - - +
88B ILE* 4.6 6.7 - - - +
89B CYS* 4.3 2.6 - - - -
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Residues in contact with ARG 82 (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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29A ARG 4.6 4.0 + - - -
30A HIS 4.7 8.7 + - - -
31A LEU 5.0 3.2 + - - -
32A THR* 3.1 19.4 + - - +
33A GLY* 4.0 16.5 - - - +
60B ARG* 2.6 49.0 + - - +
61B GLY* 4.1 16.8 - - - -
62B ILE* 3.3 9.6 - - + +
81B ARG* 1.3 75.6 - - - +
83B GLU* 1.3 60.9 + - - +
85B VAL* 4.2 13.4 - - + +
86B LEU* 2.7 40.5 + - - +
87B LYS* 2.9 35.6 + - - +
88B ILE 4.6 4.3 + - - -
89B CYS* 3.5 15.7 - - - +
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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