Contacts of the helix formed by residues 29 - 43 (chain A) in PDB entry 1GRB
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 29 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A GLY 3.4 5.9 + - - -
28A GLY* 1.4 76.1 - - - +
30A SER* 1.3 67.2 + - - -
31A GLY 3.4 2.7 - - - -
32A GLY 4.0 1.6 - - - +
33A LEU* 2.9 27.4 + - - +
55A GLY* 4.5 2.2 - - - -
56A GLY* 3.9 11.0 - - - -
155A ALA 4.9 0.2 + - - -
479A FAD 3.3 28.4 + - - -
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Residues in contact with SER 30 (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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29A GLY* 1.3 71.2 - - - -
31A GLY* 1.3 61.4 + - - +
33A LEU* 4.3 2.9 - - - +
34A ALA* 3.1 27.0 + - - +
55A GLY 4.3 3.5 + - - -
58A CYS* 3.6 18.5 - - - +
114A TYR* 6.5 0.7 - - - -
339A THR* 3.5 28.5 + - - +
342A ALA* 4.3 0.9 - - - -
343A ILE* 3.6 22.8 - - - +
479A FAD 3.2 19.5 + - - -
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Residues in contact with GLY 31 (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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30A SER* 1.3 74.2 - - - +
32A GLY* 1.3 64.3 + - - +
34A ALA* 4.0 0.9 - - - +
35A SER* 3.1 25.6 + - - -
155A ALA* 4.9 0.2 - - - -
329A VAL* 4.2 13.5 - - - +
342A ALA* 3.6 29.5 - - - +
343A ILE* 4.5 0.2 - - - -
346A GLY* 4.1 4.7 - - - -
479A FAD 2.9 16.6 + - - -
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Residues in contact with GLY 32 (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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25A VAL* 3.5 27.5 - - - +
27A GLY 3.5 12.5 + - - -
29A GLY 3.4 4.4 + - - +
30A SER 3.4 0.2 - - - -
31A GLY* 1.3 73.7 - - - +
33A LEU* 1.3 66.3 + - - +
35A SER* 3.5 1.0 + - - -
36A ALA* 3.1 25.3 + - - +
153A LEU* 4.4 2.2 - - - -
155A ALA* 3.8 14.8 - - - +
479A FAD 4.2 0.2 + - - -
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Residues in contact with LEU 33 (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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27A GLY 4.4 0.2 + - - -
28A GLY* 3.5 31.9 - - - +
29A GLY 2.9 19.7 + - - +
30A SER* 4.3 2.7 - - - +
32A GLY* 1.3 76.0 - - - +
34A ALA* 1.3 63.4 + - - +
36A ALA* 3.4 2.7 + - - +
37A ARG* 2.9 39.7 + - - +
48A VAL* 4.2 8.1 - - + -
54A LEU* 4.5 4.9 - - + -
55A GLY* 4.0 7.2 - - - +
114A TYR* 3.5 39.5 - - + +
118A LEU* 4.0 33.2 - - + -
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Residues in contact with ALA 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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30A SER 3.1 19.5 + - - +
31A GLY 4.0 1.3 - - - +
33A LEU* 1.3 79.6 - - - +
35A SER* 1.3 62.7 + - - +
37A ARG* 3.6 10.2 + - - +
38A ARG* 3.2 24.3 + - - +
343A ILE* 3.8 40.4 - - + +
347A ARG* 4.0 15.4 + - + +
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Residues in contact with SER 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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23A TYR* 2.8 25.0 + - - -
25A VAL* 5.0 0.2 - - - -
31A GLY 3.1 18.8 + - - -
32A GLY 3.9 0.7 - - - -
34A ALA* 1.3 74.5 - - - +
36A ALA* 1.3 59.9 + - - +
38A ARG 3.2 1.4 + - - -
39A ALA* 2.9 30.1 + - - +
153A LEU* 3.7 17.6 - - - +
346A GLY* 2.7 33.3 + - - -
349A LEU* 4.5 1.2 - - - +
350A ALA* 3.7 7.2 + - - +
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Residues in contact with ALA 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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23A TYR* 4.2 11.3 - - - -
25A VAL* 4.0 8.9 - - + +
32A GLY 3.1 17.9 + - - +
33A LEU* 3.9 3.1 - - - +
35A SER* 1.3 75.6 - - - +
37A ARG* 1.3 57.9 + - + +
39A ALA* 3.3 2.9 + - - +
40A ALA* 2.9 30.7 + - - +
46A ALA* 4.5 6.5 - - + +
48A VAL* 3.5 28.5 - - + -
118A LEU* 5.3 0.2 - - + -
123A ILE* 3.7 14.1 - - + +
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Residues in contact with ARG 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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33A LEU* 2.9 28.0 + - - +
34A ALA* 4.0 8.3 - - - +
36A ALA* 1.3 76.5 - - - +
38A ARG* 1.3 61.5 + - - +
40A ALA* 3.6 2.4 + - - +
41A GLU* 3.2 30.5 + - - +
117A ASN* 3.8 39.3 + - - +
118A LEU* 3.9 16.2 - - + -
121A SER* 4.5 13.5 + - - +
123A ILE* 3.7 20.9 - - + -
347A ARG* 4.8 13.7 - - - +
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Residues in contact with ARG 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 ALA 3.2 18.6 + - - +
37A ARG* 1.3 73.1 - - - +
39A ALA* 1.3 67.8 + - - +
41A GLU* 3.1 43.0 + - - +
42A LEU* 3.3 18.4 + - + +
347A ARG* 3.2 48.8 - - + +
350A ALA* 3.7 20.2 - - + -
351A HIS* 3.1 42.7 + - + +
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Residues in contact with ALA 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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23A TYR* 3.5 28.7 - - + -
35A SER 2.9 17.4 + - - +
36A ALA 3.6 3.4 - - - +
38A ARG* 1.3 78.0 - - - +
40A ALA* 1.3 63.4 + - - +
42A LEU* 2.9 15.9 + - - +
43A GLY 3.3 0.5 + - - -
44A ALA* 3.1 23.4 + - + +
46A ALA* 5.0 1.1 - - + -
350A ALA* 3.7 8.0 - - + +
354A PHE* 3.8 20.4 - - + +
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Residues in contact with ALA 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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36A ALA 2.9 18.0 + - - +
37A ARG 3.9 3.6 - - - +
39A ALA* 1.3 76.6 - - - +
41A GLU* 1.3 61.4 + - - +
43A GLY* 3.0 13.5 + - - -
44A ALA 3.5 18.4 + - - +
46A ALA* 5.0 2.4 - - + +
121A SER* 3.7 26.5 - - - +
122A HIS 5.6 0.7 - - - +
123A ILE* 3.9 16.8 - - + -
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Residues in contact with GLU 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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37A ARG* 3.2 20.7 + - - +
38A ARG* 3.1 42.4 + - - +
40A ALA* 1.3 76.5 - - - +
42A LEU* 1.3 66.2 + - + +
43A GLY 3.2 1.4 + - - -
121A SER* 5.8 2.5 - - - +
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Residues in contact with LEU 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 ARG* 3.4 18.8 - - + +
39A ALA 2.9 9.4 + - - +
41A GLU* 1.3 82.4 - - + +
43A GLY* 1.3 58.1 + - - +
44A ALA 3.5 1.7 + - - -
350A ALA* 3.6 26.5 - - + +
351A HIS* 4.0 19.7 - - + +
354A PHE* 3.8 25.4 - - + +
355A GLU* 4.0 35.0 - - + +
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Residues in contact with GLY 43 (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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22A ASP* 4.3 2.4 - - - +
40A ALA 3.0 11.2 + - - -
41A GLU 3.2 2.0 + - - -
42A LEU* 1.3 79.3 - - - +
44A ALA* 1.3 65.7 + - - +
45A ARG* 3.5 2.4 + - - +
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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