Contacts of the strand formed by residues 41 - 48 (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 LYS 41 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A GLU 4.1 0.3 - - - +
35A GLY* 3.4 2.8 - - - -
36A ASP* 2.8 47.0 + - + +
39A TYR* 3.1 13.9 - - + +
40A GLY* 1.4 76.9 - - - +
42A LEU* 1.4 65.2 + - - +
43A THR* 4.0 19.3 - - + -
71A PHE* 4.9 0.9 - - - +
221A LEU* 4.0 20.0 - - + -
222A GLU 3.4 4.0 - - - -
223A PHE* 3.7 30.5 - - + -
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Residues in contact with LEU 42 (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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14A ILE* 3.5 32.5 - - + -
34A GLU 3.6 1.8 - - - -
35A GLY* 3.9 3.4 - - - -
40A GLY 5.2 2.5 - - - +
41A LYS* 1.4 74.6 - - - +
43A THR* 1.4 65.8 + - - +
44A LEU* 4.0 7.2 - - + -
66A CRO 4.2 10.3 - - + -
68A VAL* 3.9 23.3 - - + +
71A PHE* 3.7 30.1 - - + -
220A LEU* 3.8 2.0 - - + +
221A LEU* 3.4 6.1 - - - +
222A GLU* 2.9 64.0 + - + +
224A VAL* 5.3 5.4 - - + -
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Residues in contact with THR 43 (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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33A GLY* 3.2 2.8 - - - -
34A GLU* 3.0 44.3 + - - +
41A LYS* 4.0 17.5 - - + -
42A LEU* 1.4 79.1 - - - +
44A LEU* 1.4 67.2 + - - +
220A LEU 3.5 5.2 - - - -
221A LEU* 3.7 21.3 - - + -
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Residues in contact with LEU 44 (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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14A ILE* 4.0 39.7 - - + -
16A VAL* 4.7 2.9 - - + -
31A GLY 4.7 2.0 - - - -
32A GLU* 3.4 14.1 - - - +
33A GLY* 3.3 24.9 - - - +
42A LEU* 4.0 11.9 - - + -
43A THR* 1.4 101.2 - - - +
45A LYS* 1.3 59.2 + - - +
46A PHE* 3.7 32.1 - - + -
66A CRO 4.7 9.9 - - + -
68A VAL* 5.9 0.2 - - + -
218A MET 4.1 0.3 - - - +
219A VAL* 3.5 6.1 - - - +
220A LEU* 2.8 39.2 + - + +
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Residues in contact with LYS 45 (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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30A SER 4.1 0.2 - - - +
31A GLY* 3.2 2.5 - - - -
32A GLU* 3.0 33.8 + - + +
44A LEU* 1.3 74.3 - - - +
46A PHE* 1.4 67.6 + - - +
47A ILE* 4.0 19.8 - - + +
210A ASP* 3.0 25.5 + - - +
213A GLU* 2.8 36.7 + - - -
215A ARG* 4.5 2.4 - - - +
217A HIS* 4.3 8.1 - - + -
218A MET 3.6 8.5 - - - +
219A VAL* 4.2 16.4 - - + +
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Residues in contact with PHE 46 (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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16A VAL* 3.9 20.0 - - + -
29A VAL* 3.9 12.6 - - + -
30A SER 3.4 2.5 - - - -
31A GLY* 3.7 17.7 - - - -
44A LEU* 3.7 29.6 - - + -
45A LYS* 1.4 72.1 - - - +
47A ILE* 1.3 65.4 + - - +
57A 32T 4.1 12.3 - - + -
64A LEU* 3.7 45.3 - - + -
66A CRO 4.0 12.1 - - + -
217A HIS* 3.0 8.7 - - - +
218A MET* 2.9 57.6 + - + +
220A LEU* 4.0 20.2 - - + -
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Residues in contact with ILE 47 (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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29A VAL* 3.4 2.9 - - - -
30A SER* 2.8 35.2 + - - +
45A LYS* 4.0 26.0 - - + +
46A PHE* 1.3 80.3 - - - +
48A CYS* 1.4 74.8 + - - +
49A THR* 3.3 10.4 + - + +
57A 32T 4.2 4.3 - - - -
213A GLU* 4.2 0.9 - - - +
215A ARG* 3.1 66.0 - - + +
216A ASP 3.6 4.3 - - - +
217A HIS* 4.2 4.5 - - + -
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Residues in contact with CYS 48 (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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27A PHE* 4.5 3.1 - - - -
28A SER 3.5 10.3 - - - -
29A VAL* 4.2 3.1 - - - -
47A ILE* 1.4 75.7 - - - +
49A THR* 1.3 61.9 + - - +
50A THR* 3.2 25.2 + - - -
51A GLY* 3.3 31.9 + - - +
52A LYS 4.1 1.6 - - - -
53A LEU* 4.0 28.3 - - + +
57A 32T 4.0 10.0 - - + +
215A ARG* 5.0 4.0 - - - +
216A ASP* 2.9 26.0 + - + +
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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