Contacts of the strand formed by residues 98 - 104 (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 PHE 98 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12I TYR* 3.6 35.9 - + - -
44I PHE* 3.2 5.2 - - - +
45I GLU 2.8 39.9 + - - +
46I THR 5.4 5.6 - - - -
49I GLY* 3.9 25.6 - - - -
50I PHE* 4.3 9.0 - + - -
67I TRP* 3.5 24.5 - + + -
96I ASN 5.4 0.9 - - - -
97I ALA* 1.3 74.4 - - - +
99I ILE* 1.3 60.8 + - - +
116I ILE* 4.2 4.9 - - + -
118I TYR 3.5 3.6 - - - -
119I LYS* 4.1 9.2 - - + -
120I PRO* 3.6 23.3 - - + -
123I TYR* 3.7 41.1 - + + -
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Residues in contact with ILE 99 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42I LEU* 4.5 10.1 - - + -
43I GLU 3.4 10.5 - - - +
44I PHE* 4.1 4.7 - - + -
87I LEU* 3.9 18.8 - - + -
90I CYS* 3.7 35.4 - - + +
91I LYS* 3.7 26.2 - - + +
94I TYR 4.4 5.2 - - - +
97I ALA* 4.1 3.6 - - + +
98I PHE* 1.3 80.4 - - - +
100I ARG* 1.3 63.0 + - - +
116I ILE* 3.6 4.3 - - - +
117I ALA* 2.7 30.6 + - + -
118I TYR* 2.9 41.3 + - + +
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Residues in contact with ARG 100 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163H ASN* 4.1 19.6 + - - +
41I CYS 3.9 0.2 - - - +
42I LEU* 3.4 6.9 - - - +
43I GLU* 2.9 61.3 + - + +
64I GLY 5.6 0.2 + - - -
65I ARG 3.1 23.2 + - - -
67I TRP* 3.4 59.7 - - + +
99I ILE* 1.3 76.5 - - - +
101I ILE* 1.3 63.4 + - - +
102I ILE* 4.1 11.5 + - + +
111I GLN* 6.0 0.6 - - - +
114I SER* 4.1 16.5 + - - -
115I PHE 3.3 19.5 - - - +
116I ILE* 4.0 6.1 - - + -
117I ALA 4.0 0.4 - - - +
183L LYS* 5.7 1.6 - - - +
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Residues in contact with ILE 101 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26I LEU* 4.6 3.1 - - + -
30I VAL* 4.3 11.4 - - + -
33I LEU* 4.2 17.0 - - + -
40I PRO* 5.2 0.4 - - + -
41I CYS 3.6 7.0 - - - +
42I LEU* 4.4 14.6 - - + -
83I VAL* 4.3 27.1 - - + -
84I LEU* 5.2 1.1 - - + -
87I LEU* 4.4 15.5 - - + -
99I ILE* 5.7 0.2 - - + -
100I ARG* 1.3 77.0 - - - +
102I ILE* 1.3 69.6 + - - +
113I ILE* 4.3 0.6 - - - +
114I SER* 3.2 4.0 + - - -
115I PHE* 2.9 60.5 + - + -
117I ALA* 3.9 24.9 - - + -
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Residues in contact with ILE 102 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33I LEU* 3.8 7.0 - - - +
40I PRO* 3.4 3.8 - - - +
41I CYS* 2.9 50.2 + - + +
43I GLU* 3.6 39.9 - - + +
100I ARG* 4.1 11.0 - - + +
101I ILE* 1.3 81.7 - - - +
103I GLY* 1.3 59.3 + - - +
104I PHE* 3.7 29.2 - - + -
111I GLN* 3.8 24.0 - - + +
113I ILE 3.3 10.1 - - - +
114I SER* 3.8 17.9 - - - +
187L ARG* 4.0 0.7 - - - +
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Residues in contact with GLY 103 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33I LEU* 3.8 20.9 - - - -
38I TRP* 4.2 4.3 - - - -
39I VAL 3.2 8.1 - - - -
102I ILE* 1.3 74.7 - - - +
104I PHE* 1.3 62.3 + - - -
111I GLN* 3.4 5.2 - - - -
112I CYS* 2.9 28.8 + - - +
113I ILE* 3.1 16.2 + - - +
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Residues in contact with PHE 104 (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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37I LYS 4.6 0.5 - - - +
38I TRP* 3.2 8.6 - - - -
39I VAL* 2.8 55.3 + - + +
41I CYS* 3.8 25.1 - - + -
69I MET* 5.3 0.7 - - + -
73I PRO* 4.1 18.8 - - + -
75I PHE* 6.1 1.3 - + - -
102I ILE* 3.7 16.4 - - + -
103I GLY* 1.3 73.7 - - - -
105I ASP* 1.3 63.9 + - - +
106I SER* 3.7 5.7 + - - +
109I GLU* 6.1 2.0 - - + -
110I VAL 3.9 4.3 - - - -
111I GLN* 3.8 22.2 - - + -
184L ASN* 4.0 13.0 - - - -
187L ARG* 3.5 38.6 - - - -
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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