Contacts of the strand formed by residues 5 - 11 (chain D) in PDB entry 2RHM
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 ALA 5 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3D THR 3.9 0.4 + - - -
4D PRO* 1.3 73.1 - - - +
6D LEU* 1.3 60.2 + - - +
7D ILE* 4.0 5.8 - - + -
73D LEU* 3.8 4.2 - - - +
78D SER* 2.9 37.1 + - - +
79D LEU 3.2 5.7 + - - -
104D THR* 3.3 15.3 - - - +
106D ILE* 4.3 9.9 - - + -
185D LEU* 3.4 33.0 - - + -
186D GLN 6.1 0.4 - - - +
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Residues in contact with LEU 6 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D PRO 4.0 0.4 + - - -
5D ALA* 1.3 72.1 - - - +
7D ILE* 1.3 65.7 + - - +
8D ILE* 3.4 12.2 - - + +
73D LEU* 4.5 5.4 - - + -
79D LEU* 3.5 37.5 - - + +
81D MSE 3.8 17.0 - - + -
94D MSE 3.7 30.3 - - - -
97D LEU* 3.9 17.9 - - + -
103D PHE* 3.6 36.1 - - + -
104D THR 2.9 7.3 + - - -
105D PRO* 3.3 3.6 - - - +
106D ILE 3.0 23.3 + - - +
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Residues in contact with ILE 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D ALA* 4.7 5.2 - - + -
6D LEU* 1.3 75.0 - - - +
8D ILE* 1.3 59.8 + - - +
9D VAL* 4.3 7.0 - - + -
24D LEU* 4.3 23.8 - - + -
28D LEU* 3.8 15.9 - - + -
30D LEU* 3.4 33.0 - - + -
79D LEU 2.9 14.3 + - - +
80D ILE* 3.2 14.0 - - + +
81D MSE 2.9 27.7 + - - +
106D ILE* 3.2 21.3 - - + +
108D ILE* 4.7 8.3 - - + -
181D VAL* 3.8 19.7 - - + -
185D LEU* 4.8 7.0 - - + -
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Residues in contact with ILE 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D LEU* 3.4 30.7 - - + +
7D ILE* 1.3 72.5 - - - +
9D VAL* 1.3 64.8 + - - +
10D THR* 4.5 1.6 - - - -
81D MSE 3.5 5.4 - - + +
85D PHE* 3.5 31.2 - - + -
94D MSE 4.0 19.1 - - + -
105D PRO* 4.0 11.0 - - + -
106D ILE 2.8 15.7 + - - +
107D GLN* 3.3 22.4 - - + +
108D ILE 2.8 28.2 + - - +
155D LEU* 4.5 8.7 - - + -
157D LEU* 3.7 24.7 - - + -
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Residues in contact with VAL 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D ILE* 4.3 4.0 - - + -
8D ILE* 1.3 75.4 - - - +
10D THR* 1.3 61.4 + - - +
17D LYS* 3.9 31.9 - - + +
20D LEU* 4.0 17.0 - - + -
21D SER* 4.1 10.3 - - - -
24D LEU* 3.8 28.5 - - + -
80D ILE* 3.9 17.7 - - + -
81D MSE 2.9 11.2 + - - +
82D GLU* 3.3 6.2 - - + +
83D SER 3.2 25.1 + - - +
85D PHE* 3.6 2.1 - - - -
108D ILE* 3.4 11.2 - - + +
110D CYS* 4.2 5.4 - - - -
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Residues in contact with THR 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D ILE* 4.0 2.0 + - - -
9D VAL* 1.3 73.2 - - - +
11D GLY* 1.3 64.2 + - - +
17D LYS* 4.1 5.0 - - - +
83D SER 3.2 7.2 - - - -
85D PHE* 3.3 35.8 + - - +
107D GLN* 3.7 24.5 - - - +
108D ILE 2.9 15.7 + - - +
109D ARG* 3.5 19.4 - - + -
110D CYS* 2.8 30.5 + - - +
152D ILE* 3.8 13.0 - - + +
153D PRO 5.2 0.7 + - - -
154D PRO* 4.7 5.4 - - + -
155D LEU* 5.3 0.8 - - - +
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Residues in contact with GLY 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D THR* 1.3 82.8 + - - +
12D HIS* 1.3 68.4 + - - -
15D THR* 3.6 6.1 - - - -
17D LYS* 3.2 8.1 - - - +
83D SER 3.8 0.4 + - - -
84D ASN* 3.1 21.0 - - - +
110D CYS 3.5 17.0 - - - -
152D ILE* 3.5 14.8 - - - +
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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