Contacts of the helix formed by residues 110 - 120 (chain D) in PDB entry 1THF
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 PRO 110 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106D ALA 3.2 14.8 - - - +
107D VAL 3.7 10.8 - - - +
108D GLU 3.9 2.0 - - - +
109D ASN* 1.3 87.8 - - - +
111D SER* 1.3 60.8 + - - +
113D ILE* 3.1 28.9 + - + +
156D TRP* 4.0 22.4 - - + -
159D GLU* 4.9 1.8 - - + -
163D ARG* 3.6 35.8 - - + +
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Residues in contact with SER 111 (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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109D ASN* 3.0 17.4 + - - +
110D PRO* 1.3 74.8 - - - +
112D LEU* 1.3 64.1 + - - +
113D ILE 3.2 0.4 - - - -
114D THR* 3.1 12.0 + - - -
115D GLN* 2.9 36.3 + - - +
163D ARG* 3.8 21.4 - - - +
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Residues in contact with LEU 112 (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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84D HIS 4.7 0.4 - - - +
85D ASP* 4.0 13.0 - - - +
86D PHE* 3.5 39.9 - - + +
102D ILE* 4.1 18.6 - - + -
105D ALA* 3.7 35.2 - - + +
106D ALA* 5.0 0.7 - - - -
109D ASN* 2.8 27.7 + - + +
111D SER* 1.3 78.5 + - - +
113D ILE* 1.3 63.5 + - - +
115D GLN* 3.3 13.2 + - - +
116D ILE* 3.1 36.6 + - + +
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Residues in contact with ILE 113 (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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102D ILE* 4.0 15.7 - - + -
106D ALA* 4.0 15.0 - - + -
110D PRO 3.1 14.8 + - - +
112D LEU* 1.3 78.4 - - - +
114D THR* 1.3 58.0 + - - +
116D ILE* 3.4 3.1 + - - +
117D ALA* 3.0 26.3 + - - +
125D VAL* 4.1 7.8 - - + +
127D VAL* 3.7 25.8 - - + -
156D TRP* 4.2 9.0 - - + -
160D VAL* 4.2 18.2 - - + -
163D ARG* 3.7 21.3 - - + +
165D ALA* 3.5 38.8 - - + +
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Residues in contact with THR 114 (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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111D SER* 3.1 14.8 + - - -
113D ILE* 1.3 73.3 - - - +
115D GLN* 1.3 61.2 + - - +
117D ALA* 3.7 3.3 - - + +
118D GLN* 2.8 63.5 + - + +
163D ARG* 2.6 45.6 + - - +
164D GLY* 5.7 0.4 - - - -
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Residues in contact with GLN 115 (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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86D PHE* 3.6 36.1 - - + +
109D ASN* 4.4 6.6 + - - +
111D SER* 2.9 36.5 + - - +
112D LEU* 3.3 14.1 + - - +
114D THR* 1.3 77.1 - - - +
116D ILE* 1.3 61.9 + - - +
118D GLN* 3.5 9.9 + - - +
119D THR* 3.1 28.9 + - - -
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Residues in contact with ILE 116 (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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86D PHE* 4.0 21.8 - - + -
89D ALA* 3.6 25.4 - - + -
93D ILE* 3.9 27.4 - - + -
100D VAL* 4.2 10.8 - - + -
102D ILE* 4.0 18.4 - - + -
112D LEU* 3.1 32.6 + - + +
113D ILE 3.9 2.9 - - - +
115D GLN* 1.3 75.1 - - - +
117D ALA* 1.3 58.4 + - - +
119D THR 3.3 0.7 + - - -
120D PHE* 2.9 35.2 + - + +
121D GLY 4.1 0.2 - - - +
124D ALA* 4.6 2.9 - - + +
125D VAL* 4.1 17.5 - - + -
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Residues in contact with ALA 117 (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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113D ILE 3.0 17.1 + - - +
114D THR* 3.7 6.3 - - + +
116D ILE* 1.3 78.3 - - - +
118D GLN* 1.3 58.2 + - + +
121D GLY* 2.8 38.6 + - - -
122D SER* 3.6 15.2 + - - +
125D VAL* 4.0 4.4 - - + +
164D GLY* 3.4 28.3 - - - +
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Residues in contact with GLN 118 (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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114D THR* 2.8 48.5 + - + +
115D GLN* 4.0 9.3 - - - +
117D ALA* 1.3 76.3 - - + +
119D THR* 1.3 62.6 + - - +
121D GLY 4.6 0.9 + - - -
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Residues in contact with THR 119 (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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86D PHE* 3.6 16.2 - - + -
115D GLN 3.1 17.8 + - - -
118D GLN* 1.3 79.8 - - - +
120D PHE* 1.3 94.5 + - + +
121D GLY 3.7 0.2 - - - -
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Residues in contact with PHE 120 (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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86D PHE* 4.3 4.3 - + - -
90D SER* 3.4 46.9 - - - -
93D ILE* 3.5 37.2 - - + -
94D LEU* 4.2 22.2 - - + -
116D ILE* 2.9 22.5 + - + +
119D THR* 1.3 101.6 - - + +
121D GLY* 1.3 60.7 + - - +
124D ALA* 3.8 23.9 + - + +
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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