Contacts of the helix formed by residues 88 - 95 (chain D) in PDB entry 4EOZ
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 88 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46D ARG* 6.2 2.0 - - - +
84D HIS* 2.8 41.6 + - + +
87D ASN* 1.3 78.0 - - + +
89D VAL* 1.3 66.5 + - + +
90D ARG 3.5 0.4 - - - -
91D GLU* 3.6 2.9 + - - +
92D ASP* 2.3 51.2 + - - +
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Residues in contact with VAL 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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84D HIS* 2.7 36.9 + - + +
85D LEU* 3.2 45.3 - - + -
88D LYS* 1.3 72.7 - - + +
90D ARG* 1.3 65.1 + - - +
91D GLU 3.4 0.3 + - - -
92D ASP* 3.5 10.7 + - - +
93D VAL* 3.4 17.2 + - - +
108D ALA* 4.1 24.6 - - + +
112D HIS* 6.4 0.2 - - + -
147D PHE* 4.1 5.6 - - + -
151D VAL* 4.0 14.8 - - + -
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Residues in contact with ARG 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 LEU 2.7 19.7 + - - +
86D ILE* 3.4 35.7 + - - +
88D LYS 3.5 0.4 - - - -
89D VAL* 1.3 74.9 - - - +
91D GLU* 1.3 58.1 + - - +
93D VAL* 3.3 7.1 + - - +
94D LEU* 3.0 49.1 + - + +
150D GLN* 2.6 55.4 + - - +
151D VAL* 4.6 5.6 - - - -
154D TYR* 3.3 42.0 + - - -
157D ILE* 4.1 11.7 - - + -
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Residues in contact with GLU 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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86D ILE 4.3 2.6 + - - +
87D ASN 3.6 22.2 - - - +
88D LYS 3.6 3.1 + - - +
89D VAL 3.2 0.6 - - - -
90D ARG* 1.3 76.6 - - - +
92D ASP* 1.3 65.3 + - - +
94D LEU* 4.4 13.1 - - - +
95D ASN* 2.7 56.6 + - - +
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Residues in contact with ASP 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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88D LYS* 2.3 47.7 + - - +
89D VAL* 3.7 11.5 - - + +
90D ARG 3.3 0.4 - - - -
91D GLU* 1.3 79.6 - - - +
93D VAL* 1.3 64.4 + - + +
95D ASN* 3.5 9.9 + - - +
96D SER* 3.3 15.9 + - - -
104D THR* 3.5 13.1 - - + +
108D ALA* 6.0 2.5 - - + -
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Residues in contact with VAL 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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89D VAL 3.4 16.2 - - - +
90D ARG 3.3 7.1 + - - +
92D ASP* 1.3 78.5 - - + +
94D LEU* 1.3 56.9 + - - +
96D SER* 2.5 31.0 + - - +
97D LEU* 3.7 2.5 + - - +
101D PHE* 3.5 31.1 - - + -
104D THR* 4.0 4.7 - - + +
105D LEU* 4.4 31.2 - - + -
108D ALA* 4.4 13.2 - - + -
151D VAL* 4.5 7.9 - - + -
157D ILE* 3.8 24.0 - - + -
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Residues in contact with LEU 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 ARG* 3.0 44.4 + - + +
91D GLU* 4.1 14.1 - - - +
93D VAL* 1.3 72.6 - - - +
95D ASN* 1.3 61.3 + - - +
96D SER 3.1 7.6 + - - -
97D LEU* 3.4 29.7 + - + +
154D TYR* 4.2 11.9 - - + +
156D CYS* 4.2 25.4 - - + -
157D ILE* 3.5 28.0 - - + -
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Residues in contact with ASN 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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91D GLU* 2.7 44.4 + - + +
92D ASP* 3.7 6.7 - - - +
93D VAL 3.3 0.4 - - - -
94D LEU* 1.3 78.0 - - - +
96D SER* 1.3 58.0 + - - +
97D LEU 3.8 0.7 - - - -
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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