Contacts of the helix formed by residues 33 - 42 (chain A) in PDB entry 1H9T
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 ALA 33 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A PRO* 1.3 72.9 - - - +
34A GLU* 1.3 67.7 + - - +
35A ARG* 2.8 13.8 + - + +
36A GLU* 2.9 20.1 + - + +
37A LEU* 2.8 20.1 + - - +
5Y T 3.7 36.9 + - + +
6Y G 3.6 13.9 - - - +
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Residues in contact with GLU 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A PRO 3.4 3.8 + - - +
33A ALA* 1.3 69.8 - - - +
35A ARG* 1.3 56.0 + - + +
37A LEU* 4.5 1.3 - - - -
38A SER* 3.0 28.6 + - - -
45A ARG* 3.4 35.3 + - + +
48A LEU* 3.2 16.5 - - + +
49A ARG* 2.8 46.1 + - - -
52A LEU* 3.9 21.1 - - + +
63A ILE* 5.1 2.8 - - - +
69A THR* 4.9 3.1 + - - +
6Y G 3.1 39.1 + - - +
7Y G 3.5 6.4 + - - -
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Residues in contact with ARG 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ALA* 2.8 12.2 + - + -
34A GLU* 1.3 74.2 - - + +
36A GLU* 1.3 68.2 + - - +
38A SER* 3.0 22.2 + - - -
39A GLU* 3.1 8.2 + - - +
45A ARG* 4.0 31.2 - - - +
13X C 3.8 18.4 - - - +
14X C 5.0 0.8 - - - +
5Y T 3.7 24.6 + - - +
6Y G 3.0 44.5 + - - +
7Y G 4.2 0.6 + - - -
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Residues in contact with GLU 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A PRO* 3.7 24.1 - - + +
33A ALA* 2.9 25.3 + - + +
35A ARG* 1.3 81.3 - - - +
37A LEU* 1.3 51.9 + - - +
39A GLU* 3.3 9.1 + - + +
40A LEU* 2.8 43.8 + - + +
5Y T 5.6 0.5 + - - -
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Residues in contact with LEU 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A TYR* 5.5 0.2 - - + -
16A ILE* 4.6 13.7 - - + -
25A PHE* 4.7 15.5 - - + -
31A LEU* 3.1 38.4 - - + -
32A PRO* 3.7 20.4 - - + +
33A ALA 2.8 18.3 + - - +
34A GLU* 4.5 0.4 - - - -
36A GLU* 1.3 73.9 - - - +
38A SER* 1.3 57.3 + - - +
40A LEU* 4.0 10.8 - - + -
41A ILE* 2.8 60.1 + - + +
48A LEU* 4.0 14.8 - - + -
52A LEU* 5.2 1.1 - - + -
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Residues in contact with SER 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A GLU 3.0 16.7 + - - -
35A ARG* 3.0 13.5 + - - -
37A LEU* 1.3 74.7 - - - +
39A GLU* 1.3 57.1 + - - +
41A ILE* 2.9 4.6 + - - +
42A GLY 2.7 32.6 + - - -
43A VAL* 3.2 21.4 + - - -
44A THR* 4.2 1.5 - - - -
45A ARG* 3.7 27.0 + - - +
48A LEU* 3.7 11.4 - - - +
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Residues in contact with GLU 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ARG 3.1 6.6 + - - +
36A GLU* 3.7 11.2 - - + +
38A SER* 1.3 79.8 + - - +
40A LEU* 1.3 78.7 + - - +
42A GLY* 3.1 13.9 + - - +
43A VAL 4.7 1.8 - - - -
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Residues in contact with LEU 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A TYR* 3.7 23.1 - - + +
24A ARG* 4.9 5.4 - - - +
25A PHE* 5.0 15.5 - - + -
32A PRO* 5.4 3.1 - - + -
36A GLU* 2.8 25.6 + - + +
37A LEU* 3.4 18.6 - - + +
39A GLU* 1.3 89.6 - - + +
41A ILE* 1.3 63.3 + - - +
42A GLY* 4.4 0.2 - - - -
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Residues in contact with ILE 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A PHE* 4.4 18.7 - - + -
12A ALA* 3.9 17.3 - - + +
15A TYR* 3.6 38.8 - - + +
16A ILE* 3.7 28.0 - - + -
37A LEU* 2.8 43.4 + - + +
38A SER* 3.6 3.1 - - - +
40A LEU* 1.3 75.0 - - + +
42A GLY* 1.3 60.3 + - - +
43A VAL* 3.3 27.1 - - + -
48A LEU* 4.9 5.2 - - + -
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Residues in contact with GLY 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A SER 2.7 13.8 + - - -
39A GLU* 3.1 12.1 + - - -
40A LEU 4.4 0.2 - - - -
41A ILE* 1.3 75.7 - - - +
43A VAL* 1.3 61.2 + - - +
9X A 4.5 5.9 + - - -
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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