Contacts of the helix formed by residues 81 - 87 (chain D) in PDB entry 2J3W
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 VAL 81 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59D PHE* 3.6 23.8 - - + -
63D SER* 4.6 12.8 - - - +
76D ASP 5.1 0.2 - - - -
77D VAL* 2.8 35.8 + - + +
80D LYS* 1.3 80.9 - - + +
82D ALA* 1.3 70.1 + - - +
83D PHE 3.3 1.6 - - - -
84D LYS* 3.1 6.3 + - - +
85D MET* 3.0 31.1 + - + +
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Residues in contact with ALA 82 (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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59D PHE* 3.7 24.9 - - + -
77D VAL 2.8 6.1 + - - +
78D ILE* 3.3 15.9 - - - +
81D VAL* 1.3 77.8 - - - +
83D PHE* 1.3 65.4 + - - +
85D MET* 3.1 10.3 + - - +
86D TYR* 3.1 21.5 + - + +
1068D PLM 3.6 37.7 - - + -
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Residues in contact with PHE 83 (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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78D ILE* 2.9 54.2 + - + +
79D ALA* 3.8 4.0 - - - +
82D ALA* 1.3 72.7 - - - +
84D LYS* 1.3 60.2 + - - +
85D MET 3.0 0.2 + - - -
87D LEU* 2.7 48.6 + - + -
88D GLY 3.0 2.6 + - - -
89D ILE* 3.1 38.4 - - + +
91D PRO* 3.7 12.1 - - + -
105D LEU* 4.2 16.8 - - + -
107D LEU* 4.0 18.4 - - + -
131D LEU* 4.6 17.0 - - + -
135D LEU* 4.2 11.9 - - + -
163D ILE* 5.4 3.8 - - + -
1068D PLM 3.7 24.2 - - + -
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Residues in contact with LYS 84 (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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13D LYS* 4.3 7.7 - - - +
79D ALA 4.4 0.6 + - - -
80D LYS 4.0 12.3 - - - +
81D VAL* 3.1 8.9 + - - +
83D PHE* 1.3 74.4 - - - +
85D MET* 1.3 58.9 + - - +
88D GLY* 2.9 23.1 + - - -
89D ILE 2.6 28.6 + - - +
90D THR* 3.7 18.6 - - - +
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Residues in contact with MET 85 (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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13D LYS* 3.1 27.3 + - - +
59D PHE* 3.6 24.0 - - + -
62D ARG* 4.6 36.3 - - + +
63D SER* 4.8 4.3 - - - -
81D VAL* 3.0 20.3 + - + +
82D ALA 3.3 9.9 - - - +
84D LYS* 1.3 78.0 - - - +
86D TYR* 1.3 87.7 + - + +
88D GLY 4.6 0.2 + - - -
25F SER* 3.0 20.2 - - - +
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Residues in contact with TYR 86 (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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55D LEU* 3.6 39.1 + - + -
58D ASP* 2.7 28.0 + - - -
59D PHE* 3.5 32.4 + + - +
62D ARG* 5.5 1.6 - - - -
82D ALA* 3.1 20.2 + - + +
85D MET* 1.3 101.1 - - + +
87D LEU* 1.3 62.6 + - + +
88D GLY 3.6 0.4 - - - -
1068D PLM 3.9 20.9 - - + -
24F VAL* 3.0 28.2 - - - +
25F SER* 3.1 20.1 + - - -
27F SER* 4.2 11.4 - - - -
28F ALA* 3.7 19.1 - - + +
31F LEU* 4.4 3.8 - - + -
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Residues in contact with LEU 87 (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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19D PHE* 3.8 28.3 - - + -
83D PHE* 2.7 28.6 + - + +
86D TYR* 1.3 79.7 - - - +
88D GLY* 1.3 62.2 + - - +
89D ILE* 3.3 24.3 + - + +
110D ASN* 4.7 5.8 - - - +
111D PRO* 3.9 23.9 - - + +
112D LEU* 5.3 2.7 - - + -
131D LEU* 3.9 17.0 - - + -
1068D PLM 3.6 47.1 - - + -
22F THR* 4.2 6.2 - - - +
23F GLU 4.0 7.1 - - - +
24F VAL* 4.4 4.2 - - + +
28F ALA* 5.0 0.4 - - + -
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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