Contacts of the helix formed by residues 87 - 97 (chain D) in PDB entry 3RMD
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 ASP 87 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85D MET* 3.3 23.4 - - - +
86D ASP* 1.3 78.9 + - - +
88D PHE* 1.3 64.4 + - - +
89D LYS* 2.8 30.4 + - - +
90D LEU* 3.0 34.7 + - + +
91D ALA 3.3 0.5 + - - -
363D LYS* 2.9 33.6 + - - +
576D ARG* 5.7 0.4 - - - +
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Residues in contact with PHE 88 (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 GLN* 3.1 30.9 - - - +
15D ILE* 5.4 0.7 - - - -
33D TYR* 4.2 5.5 - + + -
35D PRO* 3.4 33.9 - - + -
37D LEU* 4.7 8.7 - - + -
65D MET* 3.8 24.5 - - + -
68D ALA* 3.4 26.5 - - + -
69D SER* 3.4 25.1 - - - -
72D ILE* 5.1 3.1 - - + -
85D MET 4.3 11.9 - - - -
86D ASP* 3.3 16.8 + - - -
87D ASP* 1.3 69.2 + - - +
89D LYS* 1.3 67.5 + - - +
91D ALA* 2.9 8.9 + - + +
92D TYR* 2.8 25.6 + - - +
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Residues in contact with LYS 89 (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 VAL* 3.6 26.0 - - + -
9D GLU* 4.0 9.7 + - - +
10D GLN* 3.5 34.8 + - + +
15D ILE* 5.1 7.1 - - + +
87D ASP* 2.8 30.0 + - - +
88D PHE* 1.3 75.7 - - - +
90D LEU* 1.3 61.7 + - + +
92D TYR* 3.6 7.4 - - - +
93D LEU* 2.9 34.6 + - - +
354D GLN* 3.1 41.1 - - + +
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Residues in contact with LEU 90 (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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85D MET* 4.0 27.6 - - + -
87D ASP* 3.0 34.8 + - - +
89D LYS* 1.3 84.4 - - + +
91D ALA* 1.3 57.3 + - - +
93D LEU* 3.6 5.2 - - + +
94D SER* 3.1 28.1 + - - -
352D LYS 3.7 22.6 - - - +
353D ILE* 3.9 20.6 - - + -
354D GLN* 5.0 2.2 - - + +
363D LYS* 4.1 20.4 - - + +
366D ASP* 4.5 2.2 - - - +
367D ALA* 4.0 21.1 - - + +
370D PHE* 3.8 6.4 - - + -
371D ASN* 5.5 0.5 + - - -
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Residues in contact with ALA 91 (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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33D TYR* 3.4 20.2 - - + +
35D PRO* 5.8 1.6 - - + -
36D SER 6.3 0.2 - - - +
85D MET* 4.4 14.6 - - + +
87D ASP 3.3 5.2 + - - +
88D PHE* 2.9 14.6 + - + +
90D LEU* 1.3 77.5 - - - +
92D TYR* 1.3 56.3 + - - +
94D SER* 2.7 22.2 + - - -
95D ASP* 2.8 25.8 + - - +
370D PHE* 3.8 10.5 - - + -
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Residues in contact with TYR 92 (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 VAL* 4.2 14.1 - - + -
15D ILE* 3.3 41.5 - - + +
17D GLU* 2.6 32.7 + - - -
29D ARG* 3.8 8.7 + - - -
31D VAL* 3.5 18.4 - - + +
33D TYR* 3.4 38.7 + + + -
88D PHE 2.8 19.4 + - - +
89D LYS* 3.6 7.6 - - - +
91D ALA* 1.3 71.4 - - - +
93D LEU* 1.3 56.9 + - + +
95D ASP* 3.2 1.7 + - - +
96D THR* 2.5 75.5 + - + +
97D TYR* 5.0 0.2 - + - -
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Residues in contact with LEU 93 (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 TYR* 3.4 42.8 - - + -
8D VAL* 3.3 44.4 - - + -
89D LYS 2.9 15.7 + - - +
90D LEU* 3.6 6.5 - - + +
92D TYR* 1.3 82.1 - - + +
94D SER* 1.3 57.8 + - - +
96D THR* 3.4 2.9 + - - -
97D TYR* 2.9 38.2 + - + +
352D LYS* 3.1 38.5 - - + +
353D ILE* 3.6 9.4 - - - +
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Residues in contact with SER 94 (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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90D LEU 3.1 15.0 + - - -
91D ALA* 2.7 17.7 + - - -
93D LEU* 1.3 76.9 - - - +
95D ASP* 1.3 62.7 + - - +
97D TYR 4.6 4.0 - - - -
98D ASN* 3.7 18.2 + - - -
352D LYS* 4.9 5.0 + - - +
370D PHE* 3.4 20.9 - - - -
371D ASN* 2.9 34.4 - - - +
374D LYS* 2.9 22.0 + - - -
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Residues in contact with ASP 95 (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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33D TYR* 2.3 40.0 + - + +
91D ALA* 2.8 12.1 + - - +
92D TYR 3.6 3.6 - - - +
94D SER* 1.3 79.8 + - - +
96D THR* 1.3 60.3 + - + +
97D TYR 3.1 0.9 - - - -
98D ASN* 3.1 24.2 - - - +
370D PHE* 5.6 0.5 - - - -
374D LYS* 3.1 23.9 + - - +
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Residues in contact with THR 96 (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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3D GLU* 5.8 0.2 - - - +
29D ARG* 5.0 5.1 + - - +
33D TYR* 5.9 0.7 - - + -
92D TYR* 2.5 73.7 + - + +
93D LEU* 3.7 0.2 - - - -
95D ASP* 1.3 76.4 - - + +
97D TYR* 1.3 89.0 + - - +
98D ASN* 3.8 2.6 + - - -
99D TYR* 4.1 7.8 + - - -
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Residues in contact with TYR 97 (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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3D GLU* 3.4 13.8 + - + -
4D PHE* 3.3 13.5 - - - -
5D TYR* 3.2 43.9 + + + -
17D GLU* 2.4 33.3 + - - -
19D TYR* 3.6 3.5 - - - +
29D ARG* 3.6 9.2 + - - -
92D TYR* 5.0 0.9 - + - -
93D LEU* 2.9 17.7 + - + +
94D SER 3.8 4.6 - - - +
95D ASP 3.1 0.2 - - - -
96D THR* 1.3 114.2 - - - +
98D ASN* 1.3 57.5 + - - +
99D TYR* 2.9 32.7 + - - +
101D ILE* 3.3 27.4 - - + -
352D LYS* 2.8 27.8 + - + -
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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