Contacts of the strand formed by residues 4 - 11 (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 PHE 4 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D MET* 4.9 6.3 - - - -
2D LYS 3.7 10.1 - - - -
3D GLU* 1.3 73.3 - - - +
5D TYR* 1.3 69.8 + - - +
6D LEU* 4.3 0.9 - - + -
19D TYR* 3.4 0.5 - - - +
20D ILE* 2.8 66.8 + - + +
97D TYR* 3.3 10.8 - - - -
101D ILE* 3.6 24.9 - - + -
102D LYS 3.3 18.6 - - - +
103D TYR* 3.5 11.0 - - + -
104D ASP* 3.4 47.6 - - + -
107D LYS* 4.2 0.2 - - + -
108D ILE* 4.1 17.9 - - + -
349D TYR* 4.3 1.1 - - + -
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Residues in contact with TYR 5 (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 PHE* 1.3 79.6 - - - +
6D LEU* 1.3 66.6 + - - +
7D THR* 4.4 4.3 - - - +
8D VAL* 4.9 2.5 - - + -
17D GLU* 3.7 11.7 - - + +
18D ARG 4.2 2.0 - - - +
19D TYR* 3.7 4.7 - - - -
93D LEU* 3.4 36.6 - - + -
97D TYR* 3.2 38.9 + + + +
101D ILE* 4.5 12.1 - - + -
348D GLY 3.4 10.9 + - - -
349D TYR* 2.5 64.9 + + - -
352D LYS* 3.4 6.6 - - + -
353D ILE 2.9 38.3 + - - -
354D GLN* 5.1 3.4 - - - -
355D ILE* 5.2 4.0 - - + +
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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 PHE* 4.3 0.7 - - + -
5D TYR* 1.3 91.0 - - - +
7D THR* 1.3 71.4 + - + +
18D ARG* 2.6 20.0 + - + +
19D TYR* 3.8 15.0 - - - +
20D ILE* 3.9 20.9 - - + -
26D GLU* 3.5 43.1 - - + +
107D LYS 5.3 0.2 - - - +
108D ILE* 3.7 33.0 - - + -
211D VAL* 3.9 25.5 - - + +
269D SER* 5.3 1.4 + - - -
349D TYR* 3.8 6.8 + - - +
355D ILE* 4.6 12.0 + - - +
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Residues in contact with THR 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 TYR* 4.9 1.6 - - - -
6D LEU* 1.3 89.4 - - + +
8D VAL* 1.3 64.6 + - - +
9D GLU* 4.7 4.3 - - - -
16D PHE 3.7 0.6 - - - +
17D GLU* 3.3 3.5 - - - -
18D ARG* 2.8 57.6 + - - +
211D VAL* 3.9 25.1 - - + +
245D HIS* 5.0 1.0 - - - -
267D GLY* 3.0 29.6 + - - +
268D ILE* 4.8 1.6 - - - -
269D SER* 4.8 9.6 - - - +
354D GLN* 6.2 1.3 - - - +
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Residues in contact with VAL 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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5D TYR* 4.9 4.7 - - + -
7D THR* 1.3 81.5 - - - +
9D GLU* 1.3 77.9 + - - +
15D ILE* 5.3 2.9 - - + -
16D PHE 3.4 4.0 - - - +
17D GLU* 3.8 24.7 - - + -
89D LYS* 3.6 17.4 - - + -
92D TYR* 4.2 12.1 - - + -
93D LEU* 3.3 42.2 - - + -
354D GLN* 3.2 31.7 - - + +
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Residues in contact with GLU 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 THR* 4.7 2.8 - - - -
8D VAL* 1.3 91.2 + - - +
10D GLN* 1.3 60.4 + - - +
11D ILE* 4.1 8.5 - - + -
15D ILE* 3.1 8.1 - - - +
16D PHE* 2.7 38.7 + - + +
89D LYS* 4.0 8.9 + - - +
245D HIS* 4.6 2.2 - - + -
266D PHE* 4.1 32.2 - - + -
267D GLY* 3.2 36.3 + - - +
268D ILE 4.6 4.1 - - - +
269D SER* 6.1 0.2 - - - -
354D GLN* 3.5 15.5 - - - +
356D GLN* 4.5 8.1 + - - -
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Residues in contact with GLN 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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9D GLU* 1.3 74.5 + - - +
11D ILE* 1.3 65.2 + - - +
12D GLY* 3.0 21.3 + - - +
14D SER 3.7 2.7 - - - +
15D ILE* 3.7 9.9 - - + -
65D MET* 3.3 28.0 - - - +
88D PHE* 3.1 40.5 - - + +
89D LYS* 3.5 26.5 + - + +
266D PHE* 4.2 10.1 - - - -
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Residues in contact with ILE 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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9D GLU* 4.4 2.9 - - + -
10D GLN* 1.3 81.3 - - - +
12D GLY* 1.3 62.1 + - - +
14D SER* 2.9 25.3 + - - +
16D PHE* 3.4 41.2 - - + -
245D HIS* 4.1 21.8 - - + +
247D LYS* 3.2 36.6 - - + -
266D PHE* 3.7 25.8 - - + -
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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