Contacts of the helix formed by residues 35 - 42 (chain E) in PDB entry 1PF7
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 LEU 35 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31E CYS* 3.5 9.5 - - + +
32E GLY* 3.2 18.6 + - - +
33E SER 3.1 10.1 - - - +
34E GLY* 1.3 80.1 - - - +
36E GLY* 1.3 63.1 + - - +
37E GLY 3.2 2.7 - - - -
38E LEU* 3.2 25.5 + - + +
114E THR* 3.7 23.1 - - + +
115E ASN 3.8 15.9 - - - +
240E LEU* 4.3 7.6 - - + -
268E ALA* 3.6 32.1 - - - +
271E LEU* 3.6 37.7 - - + -
272E GLU* 3.6 11.9 - - + +
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Residues in contact with GLY 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E CYS* 4.0 9.9 - - - +
32E GLY 4.0 0.4 + - - -
35E LEU* 1.3 74.7 - - - +
37E GLY* 1.3 52.7 + - - +
38E LEU 2.9 9.4 + - - -
39E THR* 2.6 34.5 + - - +
82E GLN* 3.5 19.6 + - - +
292E SO4 3.0 29.2 + - - -
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Residues in contact with GLY 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E GLY 4.8 1.0 + - - -
35E LEU 3.2 2.2 - - - -
36E GLY* 1.3 73.3 - - - +
38E LEU* 1.3 59.7 + - - +
39E THR* 3.0 1.1 - - - -
40E ASP* 2.8 45.9 + - - +
41E LYS* 4.0 4.2 + - - -
272E GLU* 3.5 18.9 + - - +
292E SO4 4.3 3.8 + - - -
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Residues in contact with LEU 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E ILE* 4.2 17.7 - - + -
31E CYS* 4.2 8.7 - - - -
35E LEU* 3.2 19.5 + - + +
36E GLY 2.9 1.0 + - - -
37E GLY* 1.3 77.9 - - - +
39E THR* 1.3 56.7 + - - +
40E ASP 3.0 0.2 - - - -
41E LYS* 2.9 39.4 + - + +
73E LEU* 3.7 27.1 - - + -
80E MET* 4.0 9.0 - - + +
114E THR* 5.3 4.7 - - + -
272E GLU* 3.5 41.0 + - + +
275E VAL* 3.7 30.5 - - + -
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Residues in contact with THR 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E CYS* 4.6 3.4 - - - -
36E GLY 2.6 23.8 + - - +
37E GLY* 4.3 0.2 - - - -
38E LEU* 1.3 77.9 - - - +
40E ASP* 1.3 66.2 + - - +
41E LYS 3.0 1.6 + - - -
42E LEU* 3.1 22.9 + - - +
45E ALA* 5.2 2.3 - - - +
67E ARG* 3.6 10.0 + - - -
69E VAL* 3.8 30.5 - - + +
80E MET* 3.7 30.7 - - + -
82E GLN* 3.0 28.3 + - + +
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Residues in contact with ASP 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E GLY* 2.8 30.3 + - - +
39E THR* 1.3 82.3 + - - +
41E LYS* 1.3 62.1 + - + +
42E LEU 3.4 4.9 + - - +
67E ARG* 5.3 3.5 + - - -
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Residues in contact with LYS 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E GLY 4.1 4.8 + - - -
38E LEU* 2.9 30.2 + - + +
40E ASP* 1.3 80.6 - - + +
42E LEU* 1.3 63.7 + - - +
43E THR* 3.6 7.1 + - - +
72E PHE 3.6 5.9 - - - +
73E LEU* 3.6 18.1 - - + +
269E GLN* 4.8 4.0 + - - +
272E GLU* 3.2 46.1 + - - +
273E GLN* 4.2 9.9 - - - +
276E SER* 4.2 9.9 - - - +
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Residues in contact with LEU 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E THR* 3.1 13.8 + - - +
40E ASP 4.3 5.0 - - - +
41E LYS* 1.3 80.4 - - - +
43E THR* 1.3 61.3 + - - +
45E ALA* 4.2 14.1 - - + +
69E VAL* 3.3 49.1 - - + +
70E PHE 4.0 4.9 - - - -
71E GLY* 3.7 20.2 - - - -
72E PHE 3.3 17.5 - - - +
73E LEU* 3.8 5.6 - - + -
78E CYS* 4.1 7.4 - - + -
80E MET* 3.4 37.2 - - + -
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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