Contacts of the helix formed by residues 38 - 50 (chain A) in PDB entry 2GDZ
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 ASN 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A ALA* 4.9 0.4 - - + -
15A GLN* 4.6 8.7 + - - -
36A ASP* 3.0 17.7 + - - +
37A TRP* 1.3 79.3 - - + +
39A LEU* 1.3 60.4 + - - +
40A GLU* 3.4 7.3 + - - +
41A ALA* 3.0 37.3 + - + +
42A GLY* 2.9 25.3 + - - -
60A PHE* 3.9 4.8 - - - -
300A NAD 4.0 8.3 + - - +
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Residues in contact with LEU 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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37A TRP 3.2 5.5 + - - -
38A ASN* 1.3 73.2 + - - +
40A GLU* 1.3 65.7 + - - +
42A GLY* 3.7 0.7 - - - -
43A VAL* 3.0 47.8 + - + +
60A PHE* 4.0 12.4 - - + -
62A GLN* 3.7 41.3 - - + +
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Residues in contact with GLU 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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38A ASN* 3.4 6.1 + - - +
39A LEU* 1.3 82.1 - - - +
41A ALA* 1.3 57.8 + - - +
43A VAL* 3.9 3.5 - - - +
44A GLN* 3.0 60.6 + - + +
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Residues in contact with ALA 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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14A ALA* 3.8 19.3 - - + +
15A GLN* 4.6 9.2 - - + +
38A ASN* 3.0 31.4 + - - +
40A GLU* 1.3 77.5 - - - +
42A GLY* 1.3 58.2 + - - +
44A GLN* 3.5 11.5 + - - +
45A CYS* 2.9 31.0 + - - +
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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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14A ALA* 3.6 11.5 - - - +
34A LEU* 5.5 1.4 - - - +
38A ASN 2.9 14.6 + - - -
41A ALA* 1.3 76.6 - - - +
43A VAL* 1.3 61.2 + - - +
45A CYS* 3.3 4.7 + - - +
46A LYS* 3.1 23.4 + - - +
60A PHE* 3.5 36.8 - - - -
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Residues in contact with VAL 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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39A LEU* 3.0 39.9 + - + +
40A GLU* 4.0 4.3 - - - +
42A GLY* 1.3 71.7 - - - +
44A GLN* 1.3 63.6 + - + +
46A LYS* 3.4 6.5 + - - +
47A ALA* 2.9 31.5 + - + +
60A PHE* 4.1 14.1 - - + -
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Residues in contact with GLN 44 (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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19A ARG* 5.3 0.7 - - - -
40A GLU* 3.0 46.6 + - + +
41A ALA* 3.9 9.1 - - - +
43A VAL* 1.3 79.6 - - + +
45A CYS* 1.3 56.5 + - - +
47A ALA* 3.3 7.1 + - - +
48A ALA* 2.8 32.7 + - - +
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Residues in contact with CYS 45 (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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13A ALA 4.0 4.0 - - - -
14A ALA* 3.8 13.7 - - - +
19A ARG* 3.8 39.7 - - - +
34A LEU* 3.4 29.2 - - + -
41A ALA 2.9 18.1 + - - +
42A GLY* 3.5 5.6 - - - +
43A VAL 3.3 0.2 - - - -
44A GLN* 1.3 75.2 - - - +
46A LYS* 1.3 61.7 + - - +
48A ALA* 3.2 3.1 + - - +
49A LEU* 2.9 38.6 + - - +
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Residues in contact with LYS 46 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A LEU* 5.1 6.8 - - + +
42A GLY 3.1 13.2 + - - +
43A VAL* 3.8 7.2 - - - +
45A CYS* 1.3 75.4 - - - +
47A ALA* 1.3 64.6 + - - +
49A LEU* 3.1 19.2 + - - +
50A HIS* 2.7 54.5 + - + +
55A PRO* 3.1 10.5 + - - +
58A THR* 2.7 43.1 + - - +
59A LEU* 4.1 5.8 - - - +
60A PHE* 3.8 31.0 - - + +
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Residues in contact with ALA 47 (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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43A VAL* 2.9 22.3 + - + +
44A GLN* 3.5 8.1 - - - +
46A LYS* 1.3 75.5 - - - +
48A ALA* 1.3 64.3 + - - +
50A HIS* 3.3 28.3 + - - +
51A GLU* 4.1 5.4 + - - +
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Residues in contact with ALA 48 (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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19A ARG* 3.5 25.4 - - - +
44A GLN 2.8 21.4 + - - +
45A CYS 3.2 0.6 + - - +
47A ALA* 1.3 73.2 - - - +
49A LEU* 1.3 63.2 + - - +
51A GLU* 3.2 27.1 + - - +
52A GLN* 3.8 11.4 + - - +
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Residues in contact with LEU 49 (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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19A ARG* 4.6 4.0 - - + +
22A ALA* 4.8 5.6 - - + -
23A GLU* 3.7 32.3 - - + +
26A LEU* 4.0 18.2 - - + -
34A LEU* 4.0 17.0 - - + -
45A CYS* 2.9 41.4 + - - +
46A LYS* 3.1 7.6 + - - +
48A ALA* 1.3 71.7 - - - +
50A HIS* 1.3 58.5 + - + +
51A GLU 3.1 5.6 - - - -
52A GLN* 3.1 19.5 + - - +
53A PHE* 2.9 50.3 + - + +
58A THR* 4.9 6.5 - - + -
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Residues in contact with HIS 50 (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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46A LYS* 2.7 63.8 + - + +
47A ALA* 3.3 16.1 + - - +
48A ALA 3.2 0.4 - - - -
49A LEU* 1.3 75.5 - - - +
51A GLU* 1.3 62.8 + - + +
53A PHE 3.2 17.0 + - - +
55A PRO* 3.7 37.3 - - + +
58A THR* 4.1 4.3 - - - -
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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