Contacts of the helix formed by residues 119 - 132 (chain P) in PDB entry 3PDM
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 VAL 119 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116P ASP 3.0 20.2 - - - +
118P THR* 1.3 74.4 - - + +
120P ALA* 1.3 50.7 + - - +
121P ILE 2.6 19.1 + - - -
122P HIS* 2.8 33.0 + - + +
123P LYS* 2.8 36.3 + - - +
1R G 2.7 58.1 - - + +
2R A 3.1 3.6 - - - +
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Residues in contact with ALA 120 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83P LEU* 4.3 3.8 - - - +
86P ALA* 3.0 36.5 - - + +
87P THR* 4.8 0.4 - - - -
116P ASP 4.2 1.2 + - - -
117P ALA* 4.1 3.0 + - - +
118P THR 3.7 1.4 - - - -
119P VAL* 1.3 73.2 - - - +
121P ILE* 1.3 57.4 + - - +
123P LYS* 3.9 2.2 - - - -
124P GLU* 3.3 32.3 + - + +
2R A 2.7 34.6 + - + +
3R A 4.5 9.9 - - + +
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Residues in contact with ILE 121 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35P PHE* 3.1 40.6 - - + -
41P ARG* 4.1 15.7 - - + +
44P LEU* 4.6 12.6 - - + -
83P LEU* 4.1 8.4 - - + +
86P ALA 3.6 4.5 - - - +
87P THR* 3.1 44.0 - - + -
90P LYS* 5.8 0.2 - - + -
117P ALA 3.3 17.9 - - - +
118P THR* 2.6 31.0 - - - +
119P VAL 2.6 4.9 + - - -
120P ALA* 1.3 71.5 - - - +
122P HIS* 1.3 70.0 + - - +
123P LYS 2.9 6.3 + - - -
124P GLU 3.8 0.3 + - - -
125P ILE* 3.4 20.0 + - + +
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Residues in contact with HIS 122 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31P ARG* 4.6 12.4 + - - +
34P SER* 5.4 1.2 + - - -
35P PHE* 3.2 54.9 + + + -
36P GLN* 4.7 2.5 - - + +
118P THR* 2.8 45.1 + - + +
119P VAL* 2.8 18.8 + - + +
121P ILE* 1.3 80.7 - - - +
123P LYS* 1.3 75.9 + - + +
125P ILE* 3.3 14.2 - - - +
126P ASP* 4.5 2.3 + - - -
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Residues in contact with LYS 123 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119P VAL* 2.8 36.7 + - + +
120P ALA* 4.0 2.7 - - - +
121P ILE 2.9 0.8 - - - -
122P HIS* 1.3 83.8 - - + +
124P GLU* 1.3 53.7 - - + +
125P ILE 2.2 22.8 + - - -
126P ASP* 3.0 25.7 + - - +
127P ASN* 4.5 2.5 - - - +
1R G 2.2 33.2 + - - -
2R A 2.6 61.6 + - + +
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Residues in contact with GLU 124 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78P PRO 4.6 0.2 - - - +
79P VAL* 3.5 16.3 - - - +
82P ALA* 3.1 37.6 - - - +
83P LEU* 3.3 30.3 - - + -
86P ALA* 5.6 2.1 - - + +
120P ALA* 3.3 22.4 + - + +
121P ILE 3.8 0.4 + - - -
123P LYS* 1.3 71.4 - - + +
125P ILE* 1.3 50.5 + - - +
126P ASP 3.5 0.9 - - - -
127P ASN* 3.7 21.9 + - - +
128P ILE* 2.7 37.1 + - - +
2R A 4.8 11.3 - - + +
3R A 5.5 2.3 + - - -
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Residues in contact with ILE 125 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26P ILE 5.0 0.7 - - - +
27P LEU* 3.0 57.1 - - + +
30P SER* 4.5 6.5 - - - -
31P ARG* 3.4 28.5 - - + +
35P PHE* 3.9 18.8 - - + -
44P LEU* 5.1 9.0 - - + -
83P LEU* 3.8 10.9 - - + +
121P ILE* 3.4 12.6 - - + +
122P HIS 3.3 10.5 - - - +
123P LYS 2.2 14.8 + - - -
124P GLU* 1.3 68.0 - - - +
126P ASP* 1.3 51.1 + - - +
128P ILE* 3.4 8.3 - - - +
129P LEU* 2.7 40.2 + - + +
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Residues in contact with ASP 126 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31P ARG* 4.4 12.0 + - - +
122P HIS 4.5 2.3 + - - +
123P LYS* 3.0 19.3 + - - +
125P ILE* 1.3 73.4 - - - +
127P ASN* 1.3 98.7 + - - +
128P ILE 3.1 1.8 - - - -
129P LEU* 3.3 18.8 - - + -
130P LEU* 2.8 39.6 + - + +
133P GLN* 5.7 0.2 - - - +
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Residues in contact with ASN 127 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79P VAL* 3.9 16.4 - - + +
123P LYS* 4.1 2.4 - - - +
124P GLU* 3.9 22.7 + - - +
125P ILE 3.6 0.4 - - - -
126P ASP* 1.3 104.3 + - - +
128P ILE* 1.4 51.9 + - - +
130P LEU* 3.4 10.0 - - - +
131P LEU* 2.8 47.4 + - + +
2R A 3.7 31.1 + - - +
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Residues in contact with ILE 128 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27P LEU* 4.8 11.2 - - + -
48P LEU* 6.4 1.1 - - + -
76P LEU* 3.3 30.7 - - + -
79P VAL* 3.3 38.6 - - + +
80P PHE* 3.6 21.5 - - + -
83P LEU* 4.2 13.2 - - + -
124P GLU 2.7 30.3 - - - +
125P ILE* 3.4 8.5 - - - +
127P ASN* 1.4 73.5 - - - +
129P LEU* 1.3 59.5 + - - +
130P LEU 3.0 1.6 - - - -
131P LEU* 4.0 5.4 - - + +
132P LEU* 2.8 38.5 - - + +
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Residues in contact with LEU 129 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24P LEU* 4.1 18.8 - - + +
27P LEU* 4.0 14.6 - - + +
28P VAL* 4.8 13.5 - - + +
31P ARG* 3.6 16.2 - - - +
125P ILE* 2.7 41.7 + - + +
126P ASP* 3.3 13.0 + - + -
128P ILE* 1.3 75.4 - - - +
130P LEU* 1.3 50.4 - - - +
132P LEU* 2.7 30.3 - - + +
133P GLN* 2.4 44.0 + - + +
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Residues in contact with LEU 130 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126P ASP* 2.8 34.8 + - + +
127P ASN* 3.4 8.3 - - - +
128P ILE 3.0 0.2 - - - -
129P LEU* 1.3 75.9 - - - +
131P LEU* 1.3 70.8 + - + +
132P LEU 2.9 1.8 - - - -
133P GLN* 2.8 36.8 + - + +
134P GLY* 3.3 4.0 + - - -
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Residues in contact with LEU 131 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75P THR* 3.3 40.6 - - + +
76P LEU* 4.1 9.9 - - + -
79P VAL* 3.5 28.3 - - + -
127P ASN* 2.8 41.3 + - + +
128P ILE* 3.8 3.4 - - + +
130P LEU* 1.3 74.2 - - + +
132P LEU* 1.4 50.4 + - - +
134P GLY* 2.8 27.4 + - - +
136P THR* 3.2 12.2 + - - -
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Residues in contact with LEU 132 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23P PHE* 5.1 5.4 - - + -
24P LEU* 3.8 34.8 - - + -
27P LEU* 3.8 19.1 - - + -
69P VAL* 6.2 5.6 - - + -
76P LEU* 4.4 15.6 - - + +
80P PHE* 5.6 4.9 - - + -
128P ILE* 2.8 21.0 + - + +
129P LEU* 2.7 38.8 - - + +
130P LEU 2.9 0.4 - - - -
131P LEU* 1.4 74.6 - - - +
133P GLN* 1.3 58.6 + - + +
134P GLY 2.9 16.8 + - - -
135P GLY* 4.1 4.3 + - - -
136P THR* 4.8 8.2 + - - +
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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