Contacts of the helix formed by residues 101 - 110 (chain U) 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 SER 101 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96U PHE* 4.8 2.7 - - - -
99U GLY 3.8 1.4 + - - -
100U LEU* 1.3 74.1 - - - +
102U VAL* 1.3 64.9 + - - +
103U ARG* 3.5 12.4 + - - +
104U GLU* 2.7 46.0 + - - +
105U ILE* 3.0 23.2 + - - +
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Residues in contact with VAL 102 (chain U).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41U THR* 3.7 29.4 - - + -
45U MET* 3.3 30.7 - - + +
96U PHE* 3.9 13.6 - - + -
100U LEU 3.8 1.2 + - - -
101U SER* 1.3 71.9 - - - +
103U ARG* 1.3 56.9 + - - +
106U LEU* 2.9 32.8 + - + +
316U GLU* 5.5 9.4 - - + +
317U ILE* 3.5 26.5 - - + -
320U ALA* 4.1 14.8 - - + -
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Residues in contact with ARG 103 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101U SER* 3.1 11.3 + - - +
102U VAL* 1.3 77.4 - - - +
104U GLU* 1.3 59.4 + - + +
106U LEU* 3.8 2.2 - - - +
107U ALA* 2.8 31.8 + - - +
319U ASP* 5.0 7.1 + - - +
320U ALA* 4.2 22.1 - - - +
322U GLN* 5.9 1.4 - - - +
323U PHE* 3.3 64.7 - - + +
324U ALA* 4.8 0.2 - - - +
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Residues in contact with GLU 104 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99U GLY 4.9 1.2 - - - +
100U LEU* 3.8 18.7 - - + +
101U SER* 2.7 47.9 + - - +
103U ARG* 1.3 73.8 - - + +
105U ILE* 1.3 67.0 + - - +
108U GLU* 3.0 20.6 + - - +
114U GLY 4.2 12.8 - - - +
115U GLY* 4.3 0.2 - - - -
116U CYS* 3.3 37.8 + - + +
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Residues in contact with ILE 105 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45U MET* 3.4 37.9 - - + -
92U HIS* 4.0 10.8 - - + +
95U THR* 3.6 31.6 - - + -
96U PHE* 3.7 24.2 - - + +
100U LEU* 4.0 9.2 - - + +
101U SER 3.0 14.0 + - - +
104U GLU* 1.3 78.8 - - - +
106U LEU* 1.3 63.7 + - - +
108U GLU* 3.6 2.3 - - - +
109U LEU* 3.2 32.7 + - + +
116U CYS* 4.8 0.7 - - - -
126U MET* 4.1 24.2 - - + -
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Residues in contact with LEU 106 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45U MET* 4.3 25.4 - - + +
48U LYS* 4.0 9.6 - - + -
49U ALA* 4.5 3.4 - - + +
52U LEU* 4.4 17.0 - - + -
102U VAL* 2.9 28.0 + - + +
103U ARG* 4.1 2.0 - - - +
105U ILE* 1.3 77.9 - - - +
107U ALA* 1.3 60.5 + - - +
109U LEU* 3.1 30.3 + - + +
110U THR* 3.1 15.8 + - - +
317U ILE* 4.4 3.6 - - + +
320U ALA* 4.1 9.0 - - + -
321U ALA* 3.5 40.8 - - + +
324U ALA* 3.8 12.1 - - + -
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Residues in contact with ALA 107 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103U ARG 2.8 23.5 + - - +
106U LEU* 1.3 73.2 - - - +
108U GLU* 1.3 57.2 + - - +
110U THR* 3.2 10.4 + - - +
111U GLY 2.9 22.7 + - - -
112U ARG* 3.0 18.7 + - + -
114U GLY* 3.9 7.0 - - - -
115U GLY* 3.7 22.9 - - - +
323U PHE* 4.0 15.7 - - + -
324U ALA* 3.7 9.6 - - + +
327U ASP* 5.0 0.2 - - - +
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Residues in contact with GLU 108 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104U GLU 3.0 19.4 + - - +
105U ILE 3.6 4.3 - - - +
107U ALA* 1.3 73.7 - - - +
109U LEU* 1.3 60.4 + - - +
111U GLY* 2.8 21.8 + - - -
115U GLY* 3.5 4.1 - - - -
116U CYS* 4.0 16.6 - - - +
117U ALA* 2.7 33.9 + - - -
118U LYS 3.3 0.5 + - - -
119U GLY* 3.0 26.2 + - - -
121U GLY 3.1 12.5 + - - -
122U GLY* 2.8 40.1 + - - +
126U MET* 4.2 8.7 - - + -
304X TYR* 3.4 9.4 - - - -
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Residues in contact with LEU 109 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45U MET* 6.3 1.1 - - + -
49U ALA* 4.1 15.5 - - + -
58U ILE* 3.3 38.1 - - + +
62U CYS* 5.2 0.9 - - - -
92U HIS* 3.9 26.7 - - + +
105U ILE* 3.2 19.3 + - + +
106U LEU* 3.1 18.2 + - + +
108U GLU* 1.3 77.1 - - - +
110U THR* 1.3 58.1 + - - +
111U GLY 3.2 0.2 - - - -
122U GLY 4.2 1.3 - - - +
123U SER* 3.3 40.6 - - - +
126U MET* 4.6 5.2 - - - -
304X TYR* 2.8 26.4 + - - -
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Residues in contact with THR 110 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52U LEU* 4.6 12.6 - - + -
57U ILE* 3.6 30.8 - - + +
58U ILE* 4.2 9.4 - - + -
106U LEU 3.1 13.2 + - - +
107U ALA* 3.3 10.4 + - - -
108U GLU 3.1 0.6 - - - -
109U LEU* 1.3 78.1 - - - +
111U GLY* 1.3 59.3 + - - +
112U ARG* 2.6 43.6 + - - +
324U ALA* 3.0 30.1 + - + +
325U THR* 4.8 1.3 - - + -
304X TYR* 4.4 2.2 - - - -
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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