Contacts of the helix formed by residues 99 - 103 (chain E) 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 99 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D ASN 5.7 0.2 - - - +
29D ARG* 4.7 13.0 + - + +
95D TRP* 4.1 14.0 - - + +
96D THR* 4.0 20.0 + - - +
98D ASP* 3.6 27.2 - - - +
161D ALA* 5.3 3.1 - - - -
162D TYR* 3.7 21.5 + - - +
98E LEU* 1.3 84.5 - - - +
100E SER* 1.3 86.5 + - - +
101E ASN* 3.1 31.1 + - + +
102E MET* 3.6 9.7 + - - +
126E THR* 5.4 2.6 + - - +
127E PRO 5.5 0.3 - - - +
129E ARG 4.9 1.3 - - - -
131E LEU* 4.5 5.9 - - - +
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Residues in contact with SER 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E ASN* 1.3 84.4 + - - +
101E ASN* 1.3 63.4 + - - +
102E MET 3.1 7.2 + - - -
103E VAL* 3.4 19.9 + - - +
126E THR* 4.9 1.0 + - - -
127E PRO* 3.5 37.8 + - - +
129E ARG* 3.7 37.1 + - - -
130E MET 5.4 0.2 - - - +
5G MAN 3.7 15.2 - - - -
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Residues in contact with ASN 101 (chain E).
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* 4.6 27.3 + - - +
29D ARG* 4.7 17.3 - - + +
92D SER 5.6 3.0 + - - -
95D TRP* 5.8 1.4 - - - +
96D THR* 5.8 2.2 + - - +
99E ASN* 3.1 25.9 - - + +
100E SER* 1.3 80.3 + - - +
102E MET* 1.3 57.7 + - - +
103E VAL 3.6 0.2 - - - -
105E LYS* 5.3 5.4 - - - +
127E PRO* 5.9 2.8 - - - +
5G MAN 3.1 43.4 + - - +
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Residues in contact with MET 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D ARG* 3.6 32.3 - - + -
31E LEU* 5.3 5.8 - - + -
35E LEU* 3.5 33.0 - - + -
98E LEU* 3.6 28.7 - - + -
99E ASN 3.6 7.8 + - - +
100E SER 3.1 1.4 - - - -
101E ASN* 1.3 78.0 - - - +
103E VAL* 1.3 65.6 + - - +
104E GLY 3.1 3.8 + - - -
105E LYS* 3.1 39.7 + - + +
106E ILE* 3.8 27.1 + - + +
131E LEU* 3.8 16.6 - - + -
133E ILE* 5.6 1.1 - - + -
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Residues in contact with VAL 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ARG* 4.4 1.7 + - - -
99E ASN 4.9 0.2 - - - +
100E SER* 3.4 20.1 + - - +
102E MET* 1.3 76.5 - - - +
104E GLY* 1.3 63.6 + - - +
105E LYS 3.2 0.9 + - - -
106E ILE* 3.4 17.4 + - - +
108E ILE* 3.6 24.7 - - + +
129E ARG* 4.3 25.8 - - + +
130E MET 4.6 0.7 - - - +
131E LEU* 4.4 22.0 - - + -
141E TYR* 3.4 42.0 - - + +
5G MAN 5.2 2.5 - - - -
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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