Contacts of the strand formed by residues 36 - 43 (chain H) 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 ILE 36 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34H THR 4.1 5.2 - - - +
35H ASP* 1.3 74.0 - - - +
37H LEU* 1.3 60.5 + - - +
102H ALA* 3.6 1.6 - - - -
103H TYR* 2.8 38.4 + - + +
105H LEU* 4.4 10.3 - - + -
108H PHE* 3.5 41.1 - - + -
116H MET* 5.2 6.1 - - - -
120H ILE* 3.9 26.9 - - + -
138H LEU* 4.1 16.2 - - + -
139H ARG 3.4 10.3 - - - +
140H ILE* 5.0 2.2 - - + -
141H PRO* 3.7 26.9 - - + -
144H TYR* 4.7 13.9 - - + -
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Residues in contact with LEU 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31H THR* 3.7 33.4 - - + +
35H ASP* 3.8 15.0 - - + -
36H ILE* 1.3 73.1 - - - +
38H ALA* 1.3 60.2 - - - +
85H TYR* 3.8 16.2 - - - +
101H VAL 3.4 2.5 - - - +
102H ALA* 3.8 19.3 - - + -
138H LEU* 3.1 9.6 - - - +
139H ARG* 2.8 68.9 + - + +
364H PHE* 3.7 30.1 - - + -
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Residues in contact with ALA 38 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37H LEU* 1.3 74.7 - - - +
39H ALA* 1.3 59.3 + - - +
40H PHE* 3.8 26.6 - - + -
99H CYS 3.5 1.0 - - - +
100H TYR* 3.3 6.1 - - - -
101H VAL* 2.8 34.8 + - + +
103H TYR* 3.9 15.7 - - + -
120H ILE* 4.5 0.9 - - + -
135H LEU* 3.9 5.2 - - + -
137H ASP 3.6 4.3 - - - -
138H LEU* 3.7 17.7 - - + -
364H PHE* 3.8 4.8 - - - -
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Residues in contact with ALA 39 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38H ALA* 1.3 71.2 - - - +
40H PHE* 1.3 60.3 + - - +
98H ILE* 4.4 4.9 - - + -
99H CYS 3.7 4.3 - - - -
100H TYR* 4.2 8.5 - - + -
135H LEU* 3.7 2.9 - - - +
136H GLU* 2.9 29.6 + - + +
137H ASP 3.1 13.1 + - - +
363H TYR* 3.8 32.8 - - + -
364H PHE* 3.8 19.2 - - + -
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Residues in contact with PHE 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38H ALA* 3.8 19.1 - - + -
39H ALA* 1.3 73.6 - - - +
41H ARG* 1.3 58.4 + - - +
42H VAL* 3.4 17.7 + - + +
57H VAL* 3.7 25.4 - - + -
97H TYR 3.3 1.9 - - - +
98H ILE* 3.2 6.9 - - - -
99H CYS* 2.8 41.0 + - + +
101H VAL* 4.0 16.6 - - + -
103H TYR* 3.7 14.8 - - - -
120H ILE* 3.6 35.4 - - + -
124H VAL* 4.6 0.2 - - + -
125H PHE* 4.2 18.8 - + - -
133H LEU* 3.8 24.5 - - + -
134H ARG 3.4 8.5 - - - -
135H LEU* 4.0 14.4 - - + -
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Residues in contact with ARG 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39H ALA 4.2 0.8 + - - -
40H PHE* 1.3 67.5 - - - +
42H VAL* 1.3 58.9 - - - +
43H SER* 4.1 1.1 + - - +
90H VAL* 3.8 18.2 - - - +
96H GLN* 2.9 47.4 + - + +
97H TYR 3.4 4.3 - - - -
98H ILE* 4.0 16.3 - - + +
133H LEU* 3.4 5.0 + - - -
134H ARG* 2.7 40.3 + - + +
136H GLU* 2.8 39.1 + - + +
305H LYS* 3.2 53.6 + - - +
306H ASN* 4.6 5.3 - - - +
363H TYR* 3.7 13.1 + - - -
474H THR 5.1 1.0 + - - -
475H VAL* 4.5 6.3 + - - +
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Residues in contact with VAL 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40H PHE* 3.7 16.4 - - + +
41H ARG* 1.3 71.8 - - - +
43H SER* 1.3 64.0 + - - +
44H PRO* 3.6 8.9 - - + +
53H ALA* 4.1 17.7 - - + -
54H GLY* 5.3 0.2 - - - -
57H VAL* 4.9 7.2 - - + -
96H GLN* 3.4 4.7 - - - -
97H TYR* 2.8 40.8 + - + +
99H CYS* 3.6 29.2 - - + -
130H LEU* 3.8 26.7 - - + -
133H LEU* 3.7 23.1 - - + -
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Residues in contact with SER 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41H ARG 5.0 1.2 + - - -
42H VAL* 1.3 74.2 + - - +
44H PRO* 1.3 67.0 - - - +
94H GLU 5.5 0.6 + - - -
95H ASN 3.8 7.9 - - - -
96H GLN* 3.4 27.4 + - - +
130H LEU* 3.7 1.4 - - - -
131H ARG* 2.7 34.8 + - - +
132H ALA* 3.1 34.7 + - - +
306H ASN* 4.9 2.9 + - - +
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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