Contacts of the strand formed by residues 92 - 100 (chain A) in PDB entry 1RMO
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 TYR 92 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A VAL* 4.2 3.1 - - - -
69A GLN 3.6 10.6 + - - -
70A CYS* 3.6 25.7 + - + -
83A PHE* 4.3 11.4 - + + -
84A PHE* 3.5 35.6 - + + -
87A ALA* 4.0 11.0 - - + -
88A MET* 3.4 18.4 - - + -
91A GLY* 1.3 73.1 - - - +
93A VAL* 1.4 67.8 + - - +
94A GLN* 3.8 7.9 + - - -
111A GLU* 3.6 2.1 - - - -
112A VAL* 2.8 69.2 + - + +
185A ASN* 3.4 27.4 - - - -
186A THR 3.4 18.8 - - - +
187A PRO* 4.2 2.2 - - + -
188A ILE* 3.8 4.9 - - - +
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Residues in contact with VAL 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A TYR* 1.4 73.7 - - - +
94A GLN* 1.3 65.3 + - - +
95A GLU* 3.9 20.9 - - + +
109A ARG* 3.4 33.9 - - + +
110A ALA 3.4 10.8 - - - +
111A GLU* 4.4 11.0 - - + -
184A GLN 3.7 0.5 - - - +
185A ASN* 3.1 27.4 - - - +
186A THR* 2.7 25.8 + - - +
187A PRO 5.2 0.9 - - - +
188A ILE* 3.8 21.8 - - + -
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Residues in contact with GLN 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A THR* 5.3 1.2 + - - +
66A CRO 3.0 42.1 + - - -
69A GLN* 3.6 7.1 - - - +
92A TYR* 3.8 16.1 + - + -
93A VAL* 1.3 75.1 - - - +
95A GLU* 1.4 64.8 + - - +
96A ARG* 3.4 21.9 - - + +
108A THR* 4.1 2.3 + - - +
109A ARG* 3.6 1.4 - - - -
110A ALA* 2.8 45.3 + - + +
112A VAL* 4.9 2.7 - - + -
183A GLN* 3.3 22.0 + - + +
184A GLN 3.6 2.7 - - - -
185A ASN* 2.9 27.6 + - - +
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Residues in contact with GLU 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A VAL* 3.9 21.0 - - + +
94A GLN* 1.4 77.7 - - - +
96A ARG* 1.3 65.0 + - - +
108A THR 3.3 9.4 - - - +
109A ARG* 4.3 21.4 + - + +
183A GLN* 3.3 4.3 - - - +
184A GLN* 2.9 47.0 + - + +
186A THR* 5.0 6.9 + - - +
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Residues in contact with ARG 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A THR* 2.8 30.3 + - - -
63A THR* 4.0 7.5 + - - +
66A CRO 2.7 29.1 + - - +
69A GLN* 4.1 2.0 - - - +
94A GLN* 3.4 18.3 - - + +
95A GLU* 1.3 80.3 - - - +
97A THR* 1.4 65.2 + - - +
98A ILE* 4.3 11.0 - - + -
106A TYR 4.4 0.2 - - - -
107A LYS* 3.3 4.7 - - - +
108A THR* 2.9 45.6 + - - +
165A PHE* 3.8 18.5 - - - -
181A HIS* 3.7 25.2 - - - -
182A TYR 3.2 11.0 - - - +
183A GLN* 2.8 36.4 + - + +
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Residues in contact with THR 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A ARG* 1.4 75.1 + - - +
98A ILE* 1.3 65.5 + - - +
99A PHE* 3.4 41.5 + - + -
105A ASN* 4.6 2.7 - - + -
106A TYR 3.2 9.6 - - - +
107A LYS* 3.4 34.2 + - + +
180A ASP 3.7 1.7 - - - +
181A HIS* 3.8 0.7 - - - -
182A TYR* 3.0 37.5 + - - +
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Residues in contact with ILE 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A THR 5.2 2.9 - - - +
62A THR* 4.0 3.4 - - - +
63A THR* 3.9 21.1 - - - +
96A ARG* 4.3 14.6 - - + -
97A THR* 1.3 75.8 - - - +
99A PHE* 1.3 61.6 + - - +
100A PHE* 3.7 25.2 + - + -
105A ASN* 3.1 6.2 - - - -
106A TYR* 2.8 50.7 + - + +
108A THR* 4.9 2.7 - - + -
179A ALA* 4.0 7.2 - - + -
180A ASP 3.4 3.4 - - - +
181A HIS* 3.5 51.4 - - + +
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Residues in contact with PHE 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A THR* 3.4 30.3 - - + -
98A ILE* 1.3 72.5 - - - +
100A PHE* 1.3 65.2 + - - +
101A LYS* 3.5 2.3 + - - -
105A ASN* 4.1 22.2 - - + -
107A LYS* 5.3 2.7 - - - -
178A LEU 3.8 0.2 - - - +
179A ALA* 3.4 1.9 - - - -
180A ASP* 2.9 39.9 + - + +
182A TYR* 3.8 36.6 - + + -
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Residues in contact with PHE 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A THR* 4.0 23.3 - - + -
98A ILE* 3.7 27.6 - - + -
99A PHE* 1.3 72.9 - - - +
101A LYS* 1.3 66.9 + - - +
102A ASP 3.3 0.5 + - - -
103A ASP* 2.9 32.7 + - + +
104A GLY 2.9 22.2 + - - +
106A TYR* 3.7 38.1 - + - -
130A PHE* 3.7 15.9 - + + -
136A ILE* 4.1 13.9 - - + -
169A HIS* 3.9 16.6 - + - -
177A GLN* 3.9 16.8 - - + +
178A LEU 3.6 1.6 - - - -
179A ALA* 3.6 21.3 - - + -
181A HIS* 5.8 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