Contacts of the helix formed by residues 23 - 35 (chain D) in PDB entry 3G33
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 GLY 23 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24D ASP* 1.3 65.9 + - - -
25D GLN* 3.3 3.5 + - - +
26D ARG* 3.7 38.3 + - - +
27D VAL* 3.4 18.2 + - - +
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Residues in contact with ASP 24 (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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23D GLY* 1.3 72.9 - - - +
25D GLN* 1.3 65.6 + - + +
26D ARG 3.2 0.4 - - - -
27D VAL* 3.1 18.0 + - - +
28D LEU* 3.1 20.0 + - + +
163D PHE* 4.0 27.1 - - + -
166D HIS* 4.7 21.5 + - - +
167D ARG* 5.4 2.5 - - - +
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Residues in contact with GLN 25 (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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23D GLY* 3.3 2.2 - - - +
24D ASP* 1.3 79.7 - - + +
26D ARG* 1.3 63.3 + - + +
28D LEU* 3.7 3.5 + - - +
29D GLN* 3.4 32.2 + - - +
167D ARG* 3.3 31.8 - - - +
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Residues in contact with ARG 26 (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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292A PHE* 4.7 25.0 - - - -
23D GLY 3.7 27.5 + - - +
24D ASP 3.2 1.0 - - - -
25D GLN* 1.3 78.7 - - + +
27D VAL* 1.3 63.4 + - + +
29D GLN* 3.9 14.0 + - - +
30D SER* 3.3 19.6 + - - -
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Residues in contact with VAL 27 (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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23D GLY 3.4 18.4 - - - +
24D ASP* 3.1 11.8 + - - +
26D ARG* 1.3 77.9 - - + +
28D LEU* 1.3 64.4 + - - +
30D SER* 2.6 22.9 + - - +
31D LEU* 3.0 20.7 + - + +
163D PHE* 3.5 33.0 - - + -
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Residues in contact with LEU 28 (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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24D ASP* 3.1 17.7 + - + +
25D GLN* 4.0 5.2 - - - +
26D ARG 3.5 0.2 - - - -
27D VAL* 1.3 74.5 - - - +
29D GLN* 1.3 66.1 + - + +
31D LEU* 3.2 7.5 + - + +
32D LEU* 2.9 38.7 + - + +
160D PHE* 4.3 25.8 - - + -
163D PHE* 4.2 28.9 - - + +
164D ILE* 4.9 2.7 - - + -
167D ARG* 3.8 39.5 - - - +
232D ILE* 4.3 22.9 - - + +
233D THR* 5.2 3.6 - - + -
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Residues in contact with GLN 29 (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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25D GLN* 3.4 19.3 + - - +
26D ARG* 4.1 14.2 - - - +
27D VAL 3.4 0.6 - - - -
28D LEU* 1.3 77.6 - - + +
30D SER* 1.3 62.5 + - - +
32D LEU* 3.7 11.4 - - + +
33D ARG* 3.1 28.8 + - - +
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Residues in contact with SER 30 (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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71A PHE* 3.7 26.9 - - - -
26D ARG 3.3 12.8 + - - -
27D VAL* 2.6 26.5 + - - +
29D GLN* 1.3 77.2 - - - +
31D LEU* 1.3 67.8 + - - +
33D ARG* 3.1 20.9 + - - +
34D LEU* 3.1 18.0 + - - +
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Residues in contact with LEU 31 (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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67A ARG* 4.1 15.3 - - - +
27D VAL* 3.0 30.4 + - + +
28D LEU* 3.6 6.7 - - + +
30D SER* 1.3 76.8 + - - +
32D LEU* 1.3 63.6 + - - +
34D LEU* 3.0 18.3 + - + +
35D GLU* 3.4 13.2 + - - +
155D VAL* 4.0 28.7 - - + +
159D ASP* 3.7 29.6 - - + +
160D PHE* 4.0 20.4 - - + -
163D PHE* 3.8 23.1 - - + -
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Residues in contact with LEU 32 (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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28D LEU* 2.9 30.0 + - + +
29D GLN* 3.7 9.0 - - + +
31D LEU* 1.3 75.6 - - - +
33D ARG* 1.3 64.5 + - - +
35D GLU* 3.0 45.2 + - - +
36D GLU* 4.7 2.8 + - - +
160D PHE* 3.9 10.1 - - + -
201D SER* 3.9 17.7 - - - +
232D ILE 5.0 2.9 - - - +
233D THR* 3.7 36.1 - - + +
234D GLY* 5.6 0.4 - - - -
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Residues in contact with ARG 33 (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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71A PHE* 4.7 26.8 + - + +
29D GLN* 3.1 15.6 + - + +
30D SER* 3.1 16.3 + - - +
32D LEU* 1.3 80.7 - - - +
34D LEU* 1.3 64.2 + - + +
35D GLU 3.5 0.3 + - - -
36D GLU* 4.1 20.0 + - - +
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Residues in contact with LEU 34 (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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67A ARG* 3.9 29.8 - - + +
70A ALA* 3.4 35.0 - - + -
71A PHE* 3.8 35.7 - - + -
30D SER* 3.4 15.3 - - - +
31D LEU* 3.0 10.4 + - + +
33D ARG* 1.3 79.2 - - + +
35D GLU* 1.3 67.4 + - - +
36D GLU 3.1 2.7 - - - -
37D ARG* 2.7 24.1 + - - +
38D TYR* 3.8 12.6 + - + -
155D VAL* 3.9 20.6 - - + -
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Residues in contact with GLU 35 (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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31D LEU 3.4 10.0 + - - +
32D LEU* 3.0 42.9 + - - +
34D LEU* 1.3 76.9 - - - +
36D GLU* 1.3 67.2 + - + +
38D TYR* 2.9 16.1 + - - +
39D VAL* 3.0 17.1 + - + +
155D VAL* 4.6 8.9 - - + +
160D PHE* 3.8 11.2 - - + -
199D PRO* 3.9 7.0 - - + +
200D PRO* 3.4 23.7 - - + +
201D SER* 2.7 42.4 + - - -
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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