Contacts of the helix formed by residues 88 - 93 (chain D) in PDB entry 6D6U
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 ASN 88 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95C ASP* 3.0 25.5 + - - +
157C TYR* 5.3 0.4 - - - -
158C GLY* 5.3 3.0 - - - -
87D ASN* 1.3 94.0 + - - +
89D LEU* 1.3 65.4 + - + +
90D MET 3.3 1.1 - - - -
91D ALA* 3.5 17.7 + - - +
92D SER* 4.8 0.7 + - - -
114D MET* 3.5 21.6 - - + +
115D PRO* 3.2 33.8 + - + +
116D ASN* 5.0 0.2 - - - +
117D LYS* 2.1 47.2 + - + +
118D LEU* 4.4 2.2 - - - +
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Residues in contact with LEU 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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25C ILE* 3.9 38.8 - - + -
26C ARG* 5.4 7.0 - - + -
87D ASN* 3.4 14.2 - - + +
88D ASN* 1.3 75.1 - - + +
90D MET* 1.3 64.6 + - - +
91D ALA 3.1 3.6 + - - -
92D SER* 3.3 20.5 + - - -
93D LYS* 4.6 5.9 + - - +
114D MET* 4.9 8.3 - - + -
115D PRO* 5.8 8.5 - - + -
1M NAG 6.2 0.4 - - - -
2M NAG 3.7 35.9 - - + +
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Residues in contact with MET 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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26C ARG* 4.1 26.7 - - + +
19D LEU* 4.7 4.5 - - + -
22D LEU* 4.5 10.5 - - + -
23D LEU* 3.5 47.1 - - + -
86D LEU* 3.5 39.9 - - + -
87D ASN* 4.0 7.2 + - - +
88D ASN 3.3 0.6 - - - -
89D LEU* 1.3 79.0 - - - +
91D ALA* 1.3 60.9 + - - +
92D SER 3.1 1.0 + - - -
93D LYS* 3.3 19.4 + - + +
94D ILE* 3.7 26.3 + - + +
119D LEU* 3.7 14.6 - - + +
121D ILE* 5.2 2.5 - - + -
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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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87D ASN 4.6 0.4 + - - -
88D ASN* 3.5 15.7 + - - +
89D LEU 3.1 1.8 - - - -
90D MET* 1.3 78.8 - - - +
92D SER* 1.3 60.0 + - - +
93D LYS 3.4 0.2 - - - -
94D ILE* 3.8 6.0 - - - +
96D THR* 3.2 26.0 - - - +
117D LYS* 4.8 12.3 - - + +
119D LEU* 3.7 22.1 - - + +
129D TYR* 3.7 29.2 - - + +
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Residues in contact with SER 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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28D ASN* 4.4 7.6 + - - -
88D ASN 4.8 0.6 + - - -
89D LEU* 3.3 14.6 + - - -
90D MET 3.1 0.2 + - - -
91D ALA* 1.3 79.7 - - - +
93D LYS* 1.3 70.9 + - - +
94D ILE 3.5 5.8 - - - +
96D THR* 5.5 1.0 + - - -
101E ASN* 5.6 2.6 + - - -
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Residues in contact with LYS 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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26C ARG* 4.1 22.1 - - - +
23D LEU* 4.2 32.1 - - + +
26D TYR* 4.1 7.7 - - - +
28D ASN* 3.1 28.6 + - - +
89D LEU 4.8 6.3 - - - +
90D MET* 3.3 14.8 + - + +
92D SER* 1.3 86.8 - - - +
94D ILE* 1.3 60.6 + - - +
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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