Contacts of the helix formed by residues 64 - 68 (chain B) in PDB entry 4RM8
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 64 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B PRO 4.5 9.6 - - - +
23B ASN* 4.1 20.4 - - - +
24B THR 3.6 10.3 - - - +
25B THR* 4.0 6.4 - - + +
63B LYS* 1.3 71.5 - - - +
65B VAL* 1.3 64.8 + - - +
66B SER* 4.1 11.0 - - - +
67B ALA* 3.2 27.5 + - + +
68B GLN* 3.0 17.3 + - - +
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Residues in contact with VAL 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B ILE* 4.2 22.2 - - + -
22B PRO 5.6 0.2 + - - -
24B THR* 3.0 22.9 + - + +
25B THR 3.9 17.3 - - - +
26B GLY* 4.0 8.3 - - - +
29B LEU* 4.4 8.3 - - + -
59B LEU* 4.2 9.8 - - + +
64B LYS* 1.3 72.9 - - - +
66B SER* 1.3 61.3 + - - +
67B ALA 3.2 1.1 + - - -
68B GLN* 4.0 11.3 + - - +
70B VAL* 3.7 21.4 - - + +
76B LEU* 4.0 26.5 - - + -
78B PHE* 4.2 18.6 - - + -
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Residues in contact with SER 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B ILE* 6.1 4.5 - - - -
22B PRO* 3.6 22.9 + - - -
64B LYS* 3.1 8.7 - - - +
65B VAL* 1.3 78.7 - - - +
67B ALA* 1.3 57.8 + - - +
68B GLN 3.4 4.0 + - - -
69B GLU 5.1 1.6 + - - -
70B VAL* 5.9 2.9 - - - -
72B LYS* 5.0 10.4 + - - +
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Residues in contact with ALA 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B LYS* 3.1 28.7 + - - -
64B LYS* 3.2 30.0 + - + +
66B SER* 1.3 80.3 + - - +
68B GLN* 1.3 58.9 + - - +
69B GLU* 4.0 3.9 - - - +
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Residues in contact with GLN 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B TYR* 2.6 33.6 + - - +
58B TRP 4.6 0.3 - - - +
59B LEU* 3.6 22.7 - - + +
60B LYS* 2.7 59.4 + - - +
63B LYS* 3.3 21.5 + - - +
64B LYS 3.0 22.2 + - - +
65B VAL* 4.0 6.5 + - - +
66B SER 3.4 3.6 + - - -
67B ALA* 1.3 85.5 - - - +
69B GLU* 1.3 76.0 + - - +
70B VAL* 3.1 3.1 - - + +
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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