Contacts of the helix formed by residues 93 - 105 (chain D) in PDB entry 3Q2T
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 93 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A ALA 3.6 16.4 - - - +
164A HIS 3.1 17.9 - - - -
166A THR* 3.1 15.9 - - + +
91D TRP 3.1 18.4 - - - +
92D THR* 1.3 73.5 - - - +
94D ASP* 1.3 64.5 + - - +
95D GLU* 3.1 4.9 + - - +
96D ASP* 2.6 55.7 + - - +
97D LEU* 2.7 13.9 + - - +
114D PHE* 4.4 1.6 - - - -
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Residues in contact with ASP 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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164A HIS 3.6 5.0 + - - +
165A ILE* 4.6 7.4 - - + +
166A THR* 2.9 41.2 + - - +
167A LYS* 4.3 7.3 + - - +
93D THR* 1.3 71.3 - - - +
95D GLU* 1.3 77.3 + - - +
97D LEU* 3.6 4.8 - - - +
98D THR* 3.0 29.0 + - - -
112D ILE* 4.1 22.2 - - + +
114D PHE* 3.8 21.7 - - + -
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Residues in contact with GLU 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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166A THR* 3.2 26.6 + - + +
167A LYS* 4.0 18.9 - - - +
93D THR* 3.1 7.3 + - - +
94D ASP* 1.3 86.5 - - - +
96D ASP* 1.3 60.8 + - + +
97D LEU 3.0 5.6 + - - -
98D THR* 3.0 19.6 + - - -
99D GLU* 3.3 8.5 + - - +
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Residues in contact with ASP 96 (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 TRP 4.0 4.0 - - - +
92D THR* 3.9 4.3 - - - +
93D THR* 2.6 66.2 + - - +
95D GLU* 1.3 74.9 - - + +
97D LEU* 1.3 61.6 + - - +
99D GLU* 3.7 29.5 - - - +
100D ALA* 3.8 5.7 + - - +
149D LEU* 4.5 7.8 - - - +
150D HIS* 4.1 16.7 + - - -
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Residues in contact with LEU 97 (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 ILE* 4.8 18.4 - - + -
88D LEU* 4.0 26.9 - - + -
92D THR* 4.7 4.5 - - + -
93D THR 2.7 17.8 + - - +
94D ASP* 3.6 4.5 - - - +
96D ASP* 1.3 77.9 - - - +
98D THR* 1.3 63.7 + - - +
99D GLU 2.9 1.8 - - - -
100D ALA* 2.5 40.2 + - + +
101D VAL* 3.3 17.7 + - + -
109D ILE* 5.6 1.3 - - + -
112D ILE* 4.2 22.4 - - + -
114D PHE* 4.7 15.5 - - + -
127D ALA* 5.6 1.8 - - + -
129D VAL* 6.2 4.0 - - + -
144D LEU* 6.4 2.0 - - + -
149D LEU* 5.0 9.0 - - + -
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Residues in contact with THR 98 (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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94D ASP* 3.0 15.0 + - - -
95D GLU* 3.4 11.2 - - - -
97D LEU* 1.3 78.3 - - - +
99D GLU* 1.3 56.6 + - - +
101D VAL* 3.0 16.7 - - + +
102D HIS* 2.9 29.2 + - + +
107D ASN* 6.0 2.5 - - - -
109D ILE* 3.1 41.5 - - + +
112D ILE* 3.9 8.3 - - - +
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Residues in contact with GLU 99 (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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95D GLU 3.3 5.4 + - - +
96D ASP* 3.7 25.1 - - - +
97D LEU 2.9 0.6 + - - -
98D THR* 1.3 78.4 - - - +
100D ALA* 1.3 57.4 + - - +
102D HIS* 3.3 18.3 + - + +
103D SER* 2.9 27.7 + - - -
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Residues in contact with ALA 100 (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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96D ASP 3.8 2.5 + - - +
97D LEU* 2.5 25.6 + - + +
99D GLU* 1.3 74.2 - - - +
101D VAL* 1.3 58.6 + - + +
103D SER* 3.0 27.8 + - - -
104D LEU* 3.2 11.7 + - - +
144D LEU* 5.0 15.2 - - + +
149D LEU* 4.1 24.0 - - + -
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Residues in contact with VAL 101 (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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97D LEU* 3.3 21.7 + - + +
98D THR* 3.0 28.3 - - + +
100D ALA* 1.3 72.0 - - + +
102D HIS* 1.3 51.8 + - + +
103D SER 3.0 4.9 - - - -
104D LEU* 3.1 12.7 + - - +
105D GLY 2.5 29.8 + - - -
106D VAL* 3.0 34.4 + - + +
107D ASN* 4.5 4.0 - - - +
109D ILE* 4.1 16.4 - - + -
140D LEU* 4.0 18.8 - - + -
144D LEU* 5.2 8.1 - - + -
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Residues in contact with HIS 102 (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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98D THR* 2.9 22.1 + - + +
99D GLU* 3.4 21.3 - - + +
100D ALA 3.2 0.2 - - - -
101D VAL* 1.3 78.4 - - + +
103D SER* 1.3 59.4 - - - +
105D GLY* 3.2 14.7 + - - +
107D ASN* 3.6 26.4 + - - +
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Residues in contact with SER 103 (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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99D GLU* 2.9 12.7 + - - -
100D ALA* 3.0 15.6 + - - -
102D HIS* 1.3 80.0 - - - +
104D LEU* 1.3 63.0 + - - +
105D GLY* 3.0 1.2 + - - -
147D ARG* 2.6 37.6 + - - -
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Residues in contact with LEU 104 (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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100D ALA 3.2 7.9 + - - +
101D VAL* 3.1 9.8 + - - +
103D SER* 1.3 82.6 + - - +
105D GLY* 1.3 63.1 + - - +
106D VAL* 4.6 8.6 - - + +
139D LYS* 4.6 16.5 + - + +
140D LEU* 4.0 16.6 - - + -
143D LEU* 4.7 16.6 - - + -
144D LEU* 3.8 43.3 - - + +
147D ARG* 3.2 44.4 - - + +
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Residues in contact with GLY 105 (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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101D VAL 2.5 10.7 + - - -
102D HIS* 3.2 17.3 - - - -
103D SER 3.0 2.5 - - - -
104D LEU* 1.3 79.6 - - - +
106D VAL* 1.3 61.8 + - - +
107D ASN* 4.3 7.6 + - - -
139D LYS* 4.4 10.9 + - - -
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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