Contacts of the strand formed by residues 39 - 45 (chain I) in PDB entry 1RBO
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 39 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37I LYS 4.9 4.0 - - - +
38I TRP* 1.3 74.6 - - - +
40I PRO* 1.3 68.2 - - - +
73I PRO* 3.8 28.5 - - + -
74I MET 3.8 13.9 - - - +
75I PHE* 3.8 33.0 - - + -
76I GLY 5.6 1.1 - - - +
103I GLY* 3.2 3.4 - - - -
104I PHE* 2.8 51.7 + - + +
106I SER* 5.5 10.1 - - - +
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Residues in contact with PRO 40 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30I VAL* 5.8 0.2 - - + -
33I LEU* 3.9 16.6 - - + -
34I LEU* 3.9 16.2 - - + -
38I TRP 3.4 9.4 - - - +
39I VAL* 1.3 84.4 - - - +
41I CYS* 1.3 62.5 + - - +
73I PRO* 3.5 1.0 - - - +
74I MET* 2.8 58.1 + - + +
77I CYS* 4.1 4.7 - - + +
83I VAL* 3.9 35.2 - - + -
101I ILE* 5.2 1.1 - - + -
102I ILE 3.4 8.1 - - - +
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Residues in contact with CYS 41 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40I PRO* 1.3 76.6 - - - +
42I LEU* 1.3 79.3 + - - +
43I GLU* 4.9 2.0 - - - -
69I MET* 4.0 26.2 - - - -
70I TRP 4.9 0.7 - - - -
72I LEU 4.5 2.9 - - - -
73I PRO* 4.0 24.0 - - + -
74I MET* 4.9 2.5 - - - +
101I ILE* 3.6 4.2 - - - +
102I ILE* 2.9 45.5 + - + +
104I PHE* 3.8 22.7 - - + -
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Residues in contact with LEU 42 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41I CYS* 1.3 90.1 - - - +
43I GLU* 1.3 64.6 + - - +
70I TRP* 2.9 47.3 + - + +
72I LEU 5.7 0.2 + - - -
74I MET* 4.9 6.5 - - - -
83I VAL* 4.1 27.6 - - + +
86I GLU* 3.7 17.7 - - + +
87I LEU* 3.6 35.9 - - + +
90I CYS* 4.2 8.1 - - + -
99I ILE* 4.5 9.6 - - + -
100I ARG 3.4 9.0 - - - +
101I ILE* 4.4 13.2 - - + -
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Residues in contact with GLU 43 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41I CYS* 4.9 4.1 - - - -
42I LEU* 1.3 79.8 - - - +
44I PHE* 1.3 62.7 + - - +
66I TYR* 6.1 0.5 - - - -
67I TRP* 3.9 22.0 + - + +
68I THR 3.1 13.0 - - - +
69I MET* 4.7 7.0 + - + +
70I TRP 4.4 0.2 - - - +
99I ILE* 3.4 5.2 - - - +
100I ARG* 2.9 71.2 + - + -
102I ILE* 3.6 25.7 - - + +
111I GLN* 5.2 1.6 + - - -
187L ARG* 2.8 32.3 + - - -
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Residues in contact with PHE 44 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43I GLU* 1.3 75.9 - - - +
45I GLU* 1.3 65.2 + - - +
46I THR* 4.8 2.0 - - + -
67I TRP* 4.0 2.9 - - - -
68I THR* 2.8 68.2 + - + +
69I MET 3.7 16.8 - - - -
70I TRP* 3.9 24.7 - + + -
90I CYS* 4.1 12.8 - - - -
94I TYR* 3.6 48.0 - + - -
97I ALA* 4.2 6.5 - - + -
98I PHE 3.2 12.3 - - - +
99I ILE* 4.1 13.5 - - + -
3S VAL* 4.0 10.5 - - + -
6S ILE* 4.3 11.7 - - + -
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Residues in contact with GLU 45 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44I PHE* 1.3 76.6 - - - +
46I THR* 1.3 63.7 + - - +
47I ASP* 3.2 13.2 + - - +
48I HIS* 2.9 53.5 + - - +
49I GLY* 4.2 1.3 - - - +
67I TRP* 3.4 36.7 - - + +
68I THR* 4.3 6.2 - - - +
97I ALA* 3.3 1.1 - - - -
98I PHE* 2.8 37.1 + - + -
227L LYS* 2.9 30.7 + - - -
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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