Contacts of the helix formed by residues 24 - 38 (chain d) in PDB entry 5GAD
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 THR 24 (chain d).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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683A U 5.1 0.5 + - - -
20d ALA 4.2 8.1 - - - +
21d ARG 3.1 1.8 + - - +
22d MET 3.1 0.4 - - - -
23d ALA* 1.3 92.6 - - + +
25d LYS* 1.3 64.1 + - - +
26d ASN* 3.0 14.1 + - - +
27d GLY* 2.9 21.7 + - - -
28d ARG* 3.1 32.5 + - - +
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Residues in contact with LYS 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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209A C 5.3 0.2 - - - +
210A C 3.1 30.1 - - - +
211A C 4.2 16.1 + - - -
1367A A 3.3 25.8 + - - +
1368A G 3.6 26.0 + - - +
24d THR* 1.3 72.7 - - - +
26d ASN* 1.3 77.4 + - - +
28d ARG* 3.2 23.6 + - - +
29d GLN* 3.0 42.4 + - - +
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Residues in contact with ASN 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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682A G 3.5 39.1 + - - +
683A U 3.3 28.0 + - - +
24d THR* 3.0 9.0 + - - +
25d LYS* 1.3 91.8 - - - +
27d GLY* 1.3 57.9 + - - +
29d GLN* 3.0 18.9 + - - +
30d VAL* 2.9 28.1 + - - +
33d ARG* 5.4 0.2 + - - -
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Residues in contact with GLY 27 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683A U 4.3 4.4 + - - -
21d ARG* 3.3 35.3 - - - +
24d THR* 2.9 11.0 + - - -
26d ASN* 1.3 74.6 - - - +
28d ARG* 1.3 65.7 + - - +
30d VAL* 3.0 13.0 + - - +
31d LEU* 2.9 24.9 + - - +
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Residues in contact with ARG 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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178A G 5.4 3.5 + - - -
179A C 4.5 19.5 + - - +
1368A G 4.5 7.3 + - - -
22d MET* 2.5 63.5 + - + +
23d ALA 3.8 4.4 + - - -
24d THR* 3.1 21.1 + - - +
25d LYS* 3.2 31.3 + - - +
27d GLY* 1.3 75.3 - - - +
29d GLN* 1.3 57.2 + - - +
31d LEU* 3.4 7.6 + - - +
32d ALA* 2.9 27.4 + - - +
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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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209A C 4.8 8.1 + - - +
210A C 3.3 21.6 + - - +
681A G 5.2 5.5 + - - -
682A G 5.3 4.2 + - - +
25d LYS* 3.0 44.7 + - + +
26d ASN* 3.0 22.0 + - - +
28d ARG* 1.3 74.5 - - - +
30d VAL* 1.3 64.5 + - - +
32d ALA* 3.3 9.0 + - - +
33d ARG* 2.9 41.6 + - - +
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Residues in contact with VAL 30 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A A 3.6 35.2 - - - +
467A G 4.4 1.6 - - - +
682A G 5.2 0.9 - - - +
683A U 4.5 16.4 - - - +
21d ARG* 4.3 19.1 - - - +
26d ASN 2.9 18.4 + - - +
27d GLY* 3.0 12.5 + - - +
29d GLN* 1.3 74.8 - - - +
31d LEU* 1.3 62.0 + - + +
33d ARG* 2.9 28.0 + - - +
34d ARG* 2.9 44.7 + - + +
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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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18d PHE* 4.4 10.3 - - + +
21d ARG* 3.6 27.4 - - + -
22d MET* 3.9 34.3 - - + +
27d GLY 2.9 15.9 + - - +
28d ARG* 3.8 5.8 - - - +
30d VAL* 1.3 80.2 - - + +
32d ALA* 1.3 56.6 + - - +
34d ARG* 4.0 5.8 - - + +
35d ARG* 3.0 52.0 + - - +
42d LEU* 3.8 21.5 - - + +
43d THR* 3.7 26.2 - - + -
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Residues in contact with ALA 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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180A G 3.6 26.8 + - - +
28d ARG 2.9 15.6 + - - +
29d GLN* 3.3 13.7 - - - +
31d LEU* 1.3 75.1 - - - +
33d ARG* 1.3 66.2 + - + +
35d ARG* 3.2 6.3 + - - +
36d ALA* 2.9 23.8 + - - +
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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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466A A 3.6 24.4 + - - -
467A G 2.8 30.7 + - - +
682A G 3.9 11.7 + - - -
26d ASN 5.4 0.2 + - - -
29d GLN* 2.9 40.8 + - - +
30d VAL* 2.9 29.1 + - - +
32d ALA* 1.3 73.4 - - + +
34d ARG* 1.3 58.1 + - - +
36d ALA* 3.2 8.2 + - - +
37d LYS* 2.9 28.6 + - - +
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Residues in contact with ARG 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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463A G 5.2 0.4 - - - +
466A A 3.7 15.4 + - - -
467A G 2.9 54.6 + - - +
30d VAL* 2.9 30.7 + - + +
31d LEU* 4.0 4.7 - - - +
33d ARG* 1.3 74.1 - - - +
35d ARG* 1.3 60.9 + - - +
37d LYS* 3.0 4.7 + - - +
38d GLY 2.8 26.0 + - - -
39d ARG* 3.5 47.3 + - + +
41d ARG 3.3 14.1 + - - -
42d LEU* 2.8 57.9 + - + +
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Residues in contact with ARG 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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53A A 4.0 33.1 + - - -
54A G 3.2 54.5 + - - +
117A G 4.5 3.6 + - - -
126A A 4.6 3.2 + - - -
179A C 5.9 1.5 - - - -
180A G 5.4 5.6 - - - +
18d PHE* 4.2 17.4 - - - -
22d MET* 4.1 13.7 - - - +
31d LEU* 3.0 39.7 + - - +
32d ALA* 3.2 6.2 + - - +
34d ARG* 1.3 76.0 - - - +
36d ALA* 1.3 59.6 + - - +
38d GLY* 3.4 11.8 + - - +
39d ARG 5.3 0.7 - - - +
42d LEU* 3.7 30.7 - - + +
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Residues in contact with ALA 36 (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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181A A 4.5 15.9 - - - +
32d ALA 2.9 16.3 + - - +
33d ARG* 3.5 8.5 - - - +
35d ARG* 1.3 75.8 - - - +
37d LYS* 1.3 63.2 + - - +
38d GLY* 3.2 2.0 + - - -
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Residues in contact with LYS 37 (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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458A G 3.3 46.6 - - + +
467A G 5.3 0.4 - - - -
468A G 2.6 31.3 + - - +
469A G 3.2 44.7 + - - +
33d ARG 2.9 14.8 + - - +
34d ARG* 3.0 6.0 + - - +
36d ALA* 1.3 77.0 - - - +
38d GLY* 1.3 63.1 + - - +
39d ARG* 3.8 23.9 - - + +
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Residues in contact with GLY 38 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A G 3.3 29.8 - - - +
34d ARG 2.8 9.5 + - - -
35d ARG* 3.8 10.8 - - - -
36d ALA 3.2 3.2 - - - -
37d LYS* 1.3 78.4 - - - +
39d ARG* 1.3 65.4 + - - +
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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