Contacts of the helix formed by residues 82 - 88 (chain T) in PDB entry 3EXG
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 THR 82 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61Q PHE* 6.5 0.4 - - + -
37T TYR* 3.8 17.9 - - - +
80T PHE* 3.6 14.8 - - - +
81T MET* 1.3 85.1 - - + +
83T PHE* 1.3 64.8 + - - +
84T ASN* 2.8 32.0 + - - +
85T PHE* 3.1 32.3 + - + +
117T PRO* 3.5 18.8 - - + -
128T HIS* 5.3 6.5 - - + +
173T GLU* 5.5 1.6 - - - +
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Residues in contact with PHE 83 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80T PHE* 4.1 15.7 - + - -
82T THR* 1.3 72.0 - - - +
84T ASN* 1.3 61.7 + - - +
86T SER* 2.5 50.7 + - - -
87T MET 3.8 1.6 + - - -
114T PHE* 3.9 20.4 - - + -
115T ARG* 3.5 7.0 - - - -
116T GLY* 3.4 28.7 - - - -
117T PRO 2.9 29.2 + - - +
118T ASN* 4.1 7.0 - - + +
132T PHE* 3.8 25.4 - - + -
136T TYR* 3.8 17.3 - + - -
168T VAL* 4.0 12.6 - - + -
169T VAL 3.4 18.6 - - - -
170T LEU* 3.8 21.8 - - + -
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Residues in contact with ASN 84 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137Q ILE* 4.5 4.5 - - + +
91R ASP* 5.1 0.9 - - - +
95R ASN* 4.5 2.3 + - - -
99R LYS* 5.3 0.5 + - - -
82T THR* 2.8 26.0 + - - +
83T PHE* 1.3 76.9 - - - +
85T PHE* 1.3 66.9 + - + +
86T SER 3.3 0.9 + - - -
87T MET* 3.3 29.4 + - + +
88T GLN* 4.9 1.0 + - - +
118T ASN* 6.3 0.6 - - - +
119T GLY 5.3 2.4 + - - +
127T GLN 3.3 22.9 - - - +
128T HIS* 3.1 27.4 + - - +
129T SER 3.5 2.1 + - - -
130T GLN* 3.2 38.4 + - - +
132T PHE* 3.7 11.4 - - - -
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Residues in contact with PHE 85 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136Q GLY 4.4 6.7 - - - -
137Q ILE* 3.3 35.4 - - + -
138Q VAL* 5.4 6.3 - - + -
28T GLU* 5.4 2.0 - - - -
59T GLU* 3.4 48.5 - - + +
80T PHE* 4.7 1.6 - - + -
81T MET* 3.7 38.1 - - + +
82T THR* 3.1 26.9 + - + +
83T PHE 3.1 1.2 - - - -
84T ASN* 1.3 75.8 - - + +
86T SER* 1.3 62.1 + - - +
87T MET 3.2 2.0 + - - -
88T GLN* 3.7 12.6 + - - +
128T HIS* 3.4 33.9 - + - -
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Residues in contact with SER 86 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80T PHE* 3.3 42.6 - - - -
82T THR 3.8 1.4 + - - -
83T PHE* 2.5 33.5 + - - +
85T PHE* 1.3 75.7 - - - +
87T MET* 1.3 58.8 + - - +
88T GLN 3.1 2.7 - - - -
89T ALA* 2.9 19.0 + - - +
90T ILE* 3.1 13.9 + - - +
93T VAL* 5.5 0.2 - - - +
132T PHE* 5.2 0.9 - - - -
136T TYR* 2.8 25.1 + - - -
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Residues in contact with MET 87 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87R MET 3.8 4.5 - - - +
88R GLN 5.0 0.3 - - - +
90R ILE* 3.7 20.6 - - + +
91R ASP* 4.1 22.4 + - + +
94R ILE* 4.1 23.3 - - + -
95R ASN* 2.6 39.9 - - - +
99R LYS* 5.0 0.2 - - - +
84T ASN* 3.3 16.9 + - + +
85T PHE 3.2 1.8 - - - -
86T SER* 1.3 78.1 + - - +
88T GLN* 1.3 60.5 + - - +
89T ALA 3.3 0.3 + - - -
90T ILE* 3.4 24.7 + - + +
130T GLN* 4.1 15.0 - - - +
132T PHE* 3.9 28.9 - - + -
135T TRP* 4.3 9.0 - - + -
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Residues in contact with GLN 88 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137Q ILE* 3.6 14.6 - - + +
138Q VAL 4.8 0.6 + - - -
172Q GLN* 3.1 22.9 + - - +
174Q GLN* 3.4 18.0 + - - +
60R MET* 3.7 24.4 - - + +
87R MET 5.2 0.9 - - - +
88R GLN 4.9 3.3 - - - +
91R ASP* 3.4 22.8 - - + +
177S GLU* 5.1 2.6 + - - -
59T GLU* 3.6 28.2 + - + +
60T MET* 3.4 37.4 - - + +
84T ASN 5.5 0.4 - - - +
85T PHE* 3.9 17.5 - - - +
87T MET* 1.3 79.5 - - + +
89T ALA* 1.3 56.9 + - - +
90T ILE 3.3 1.1 + - - -
91T ASP 4.9 0.2 + - - -
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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