Contacts of the helix formed by residues 110 - 120 (chain D) in PDB entry 3P05
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 110 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109D SER* 1.3 75.8 - - - +
111D LEU* 1.3 63.4 + - - +
112D GLN* 3.0 21.4 + - - +
113D GLU* 2.8 43.0 + - - +
114D GLN* 2.9 26.3 + - - +
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Residues in contact with LEU 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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12D HIS* 3.6 39.0 - - + +
48D THR* 4.2 9.2 - - + +
50D GLN* 3.7 37.0 - - - +
109D SER 4.2 0.2 + - - -
110D THR* 1.3 73.2 - - - +
112D GLN* 1.3 74.0 + - + +
114D GLN* 3.2 20.6 + - - +
115D ILE* 2.9 48.2 + - + +
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Residues in contact with GLN 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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110D THR* 3.0 23.7 - - - +
111D LEU* 1.3 93.1 + - + +
113D GLU* 1.3 60.7 + - + +
115D ILE* 3.4 7.9 + - - +
116D GLY* 2.9 25.6 + - - -
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Residues in contact with GLU 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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96D MET* 3.7 20.0 - - + +
97D ARG* 2.8 45.3 + - - +
108D THR 4.5 0.5 - - - +
109D SER* 3.6 1.6 - - - -
110D THR* 2.8 44.2 + - - +
112D GLN* 1.3 73.5 - - - +
114D GLN* 1.3 65.4 + - - +
116D GLY* 3.2 1.0 + - - -
117D TRP* 2.9 44.8 + - + -
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Residues in contact with GLN 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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48D THR* 3.7 9.1 - - - -
49D PRO* 3.6 27.4 - - + +
50D GLN* 3.0 37.4 + - - +
103D ASP 4.7 0.7 - - - +
106D GLY* 3.8 15.8 + - - -
109D SER* 3.2 39.1 + - - +
110D THR 2.9 17.6 + - - +
111D LEU* 3.5 9.8 - - + +
113D GLU* 1.3 75.3 - - - +
115D ILE* 1.3 63.0 + - - +
117D TRP* 3.4 13.5 + - + +
118D MET* 3.1 32.1 + - - +
126D VAL* 4.0 1.1 - - + +
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Residues in contact with ILE 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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2D ILE* 4.3 18.6 - - + -
12D HIS* 3.6 39.5 - - + +
48D THR* 4.7 1.8 - - + -
111D LEU* 2.9 35.6 + - + +
112D GLN* 3.7 7.4 - - - +
114D GLN* 1.3 74.3 - - - +
116D GLY* 1.3 60.2 + - - +
118D MET* 3.2 1.0 + - - -
119D THR* 2.8 49.7 + - + +
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Residues in contact with GLY 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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96D MET* 3.8 18.1 - - - +
112D GLN 2.9 15.5 + - - -
113D GLU 3.2 4.0 + - - -
115D ILE* 1.3 76.7 - - - +
117D TRP* 1.3 61.4 + - - +
119D THR* 3.6 4.0 + - - -
120D HIS* 3.0 26.5 + - - +
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Residues in contact with TRP 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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96D MET* 3.4 28.1 - - + +
97D ARG* 2.8 46.7 + - + -
99D PRO* 3.9 22.0 - - + +
103D ASP* 3.8 19.1 - - + -
109D SER* 3.7 26.9 - - - -
113D GLU* 2.9 47.1 + - + +
114D GLN* 3.6 11.9 - - + +
115D ILE 3.3 0.2 - - - -
116D GLY* 1.3 73.0 - - - +
118D MET* 1.3 62.1 + - - +
119D THR 3.4 0.5 + - - -
120D HIS* 3.5 11.9 + + + +
124D ILE* 2.8 58.4 + - + +
126D VAL* 4.3 16.6 - - + -
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Residues in contact with MET 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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2D ILE* 3.6 28.3 - - + -
46D GLY* 3.9 13.7 - - - +
47D ALA 3.7 20.6 - - - +
48D THR* 3.9 25.6 - - + -
49D PRO* 4.2 1.3 - - - -
114D GLN 3.1 20.9 + - - +
115D ILE 3.2 3.3 + - - +
117D TRP* 1.3 78.0 - - - +
119D THR* 1.3 58.9 + - - +
120D HIS 3.5 0.2 - - - -
123D PRO* 3.5 17.2 - - - +
124D ILE 3.6 9.0 - - - +
125D PRO* 4.5 5.1 - - + +
126D VAL* 3.6 26.7 - - + +
127D GLY* 4.1 7.0 - - - +
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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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2D ILE* 4.4 15.0 - - + -
10D MET* 4.6 24.9 - - + +
115D ILE* 2.8 35.6 + - + +
116D GLY* 3.6 4.3 + - - -
118D MET* 1.3 79.3 - - - +
120D HIS* 1.3 68.1 + - - +
121D ASN* 4.8 2.3 - - - +
123D PRO* 5.1 0.2 - - - -
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Residues in contact with HIS 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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96D MET* 4.9 22.4 + - + -
116D GLY 3.0 17.4 + - - +
117D TRP* 3.5 15.6 + + - +
119D THR* 1.3 83.5 - - - +
121D ASN* 1.3 78.5 + - - +
122D PRO* 2.7 30.5 + - + +
123D PRO* 3.1 21.3 - - - +
124D ILE* 4.7 8.7 - - + +
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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