Contacts of the helix formed by residues 19 - 31 (chain M) in PDB entry 5D4C
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 19 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17M PRO* 3.2 3.5 - - - +
18M LEU* 1.3 76.9 - - + +
20M GLU* 1.3 64.1 + - - +
21M ILE* 3.1 5.8 - - - -
22M GLN* 3.0 16.9 + - - +
23M VAL* 3.0 23.3 + - - +
123M GLU 4.5 2.8 + - - -
124M ASP* 3.2 31.9 + - - +
125M GLY* 4.8 1.3 - - - -
404M LEU* 4.0 19.3 - - + -
407M LYS* 4.2 16.4 - - + +
590M ASP* 4.3 17.1 + - + +
591M SER* 5.9 0.2 - - - -
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Residues in contact with GLU 20 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16M PRO* 4.0 7.3 - - - +
17M PRO* 3.2 41.5 + - + +
18M LEU 3.3 1.1 - - - +
19M THR* 1.3 78.3 + - - +
21M ILE* 1.3 64.6 + - + +
22M GLN 3.0 0.4 - - - -
23M VAL* 4.5 3.4 - - - +
24M GLU* 2.9 54.9 + - + +
25M SER 3.9 0.5 + - - -
459M ALA 4.5 2.5 - - - +
460M ARG* 3.2 47.8 + - - +
461M VAL 5.8 1.6 - - - +
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Residues in contact with ILE 21 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18M LEU 4.5 12.3 + - - +
19M THR* 4.6 1.1 - - - +
20M GLU* 1.3 83.5 - - + +
22M GLN* 1.3 63.8 + - + +
25M SER* 3.4 18.3 - - - -
138M SER* 3.5 25.1 + - - +
333M ILE* 5.1 2.0 - - + -
335M THR* 3.8 22.4 - - + +
336M VAL* 4.5 1.2 - - - +
407M LYS 3.7 23.1 - - - +
408M ARG* 4.8 7.4 - - + +
410M ILE* 5.5 3.8 - - + -
455M LEU* 3.7 32.3 - - + -
461M VAL* 3.8 24.7 - - + +
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Residues in contact with GLN 22 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19M THR* 3.0 9.1 + - - +
21M ILE* 1.3 82.3 + - + +
23M VAL* 1.3 66.1 + - - +
24M GLU 3.5 0.2 - - - -
25M SER* 3.2 4.0 + - - -
26M TYR 3.0 19.8 + - - -
121M MET* 3.3 19.7 - - + +
125M GLY* 3.4 26.0 - - - +
127M PHE* 4.4 3.5 - - - -
135M VAL* 4.0 10.4 - - - +
136M ILE 2.6 31.9 + - - +
137M VAL* 4.8 1.0 - - - +
138M SER* 4.6 8.5 + - - -
336M VAL* 3.3 23.7 - - - +
407M LYS* 3.4 34.9 + - + +
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Residues in contact with VAL 23 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19M THR* 3.0 20.3 + - - +
20M GLU* 4.6 4.0 - - - +
22M GLN* 1.3 79.6 - - - +
24M GLU* 1.3 69.4 + - + +
25M SER 3.2 0.2 + - - -
26M TYR* 3.3 1.4 + - - +
27M ARG* 2.9 39.2 + - + +
121M MET* 3.6 11.0 - - - -
122M THR 4.4 3.4 - - - +
123M GLU* 3.7 23.8 - - - +
125M GLY* 4.0 16.4 - - - +
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Residues in contact with GLU 24 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20M GLU* 2.9 42.2 + - + +
23M VAL* 1.3 83.2 - - + +
25M SER* 1.3 55.9 + - - +
27M ARG* 2.6 42.5 + - - +
28M ARG* 2.9 31.2 + - - +
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Residues in contact with SER 25 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20M GLU 3.9 1.6 + - - -
21M ILE 3.4 15.0 - - - -
22M GLN 3.2 9.5 + - - -
23M VAL 3.2 0.2 - - - -
24M GLU* 1.3 79.6 - - - +
26M TYR* 1.3 58.2 + - - +
28M ARG* 3.2 7.9 + - - +
29M ALA* 2.9 26.3 + - - +
335M THR* 2.6 32.2 + - - -
336M VAL* 4.1 2.9 - - - -
337M GLY* 2.8 20.8 + - - -
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Residues in contact with TYR 26 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22M GLN 3.0 7.0 + - - +
23M VAL 4.1 0.7 - - - +
25M SER* 1.3 76.7 - - - +
27M ARG* 1.3 58.1 + - - +
29M ALA* 3.3 5.0 + - + +
30M LEU* 2.9 62.2 + - + +
118M ILE* 4.2 8.0 - - - +
119M PRO* 2.5 27.2 + - - +
121M MET* 3.5 58.1 - - + -
127M PHE* 3.5 22.4 - + - -
336M VAL* 4.3 9.6 - - + -
337M GLY* 4.5 8.1 - - - -
340M MET* 4.1 29.3 - - + +
386M PHE* 4.1 7.0 - + - -
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Residues in contact with ARG 27 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23M VAL* 2.9 25.2 + - + +
24M GLU* 2.6 45.9 + - - -
26M TYR* 1.3 74.9 - - - +
28M ARG* 1.3 79.2 + - - +
30M LEU* 4.5 3.6 - - - +
31M GLN* 3.2 26.7 + - - +
33M ASP* 5.7 7.0 - - + +
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Residues in contact with ARG 28 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24M GLU* 2.9 21.4 + - - +
25M SER* 3.4 6.5 - - - +
27M ARG* 1.3 89.5 - - - +
29M ALA* 1.3 60.3 + - - +
30M LEU 3.4 0.2 - - - -
31M GLN* 3.6 31.1 - - - +
40M GLU* 3.8 29.9 + - - +
42M VAL* 3.7 40.0 - - + +
43M GLY* 4.5 2.0 - - - -
463M GLU* 3.4 33.5 + - - +
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Residues in contact with ALA 29 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25M SER 2.9 15.8 + - - +
26M TYR* 3.6 7.4 - - + +
27M ARG 3.2 0.4 - - - -
28M ARG* 1.3 79.3 - - - +
30M LEU* 1.3 62.0 + - + +
31M GLN* 5.0 0.2 - - - -
43M GLY* 3.8 9.0 - - - -
44M ILE* 3.4 30.3 + - - +
337M GLY* 3.9 22.2 - - - +
340M MET* 4.4 9.6 - - + -
341M THR* 4.0 13.7 - - - +
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Residues in contact with LEU 30 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26M TYR* 2.9 53.7 + - + +
27M ARG* 4.5 2.9 - - - +
29M ALA* 1.3 86.2 - - - +
31M GLN* 1.3 72.1 + - - +
32M ALA* 3.3 12.8 + - + +
39M ARG* 4.7 8.0 + - - -
44M ILE* 4.2 19.0 - - + +
118M ILE* 3.6 28.5 - - + -
120M LEU* 3.9 22.2 - - + -
340M MET* 4.4 9.0 - - + -
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Residues in contact with GLN 31 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27M ARG* 3.2 16.7 + - - +
28M ARG* 3.6 33.3 - - - +
29M ALA 5.0 0.2 - - - -
30M LEU* 1.3 78.0 - - - +
32M ALA* 1.3 56.7 + - - +
33M ASP* 3.1 7.9 - - - +
34M VAL* 3.1 44.4 + - + +
38M LYS 4.8 0.6 + - - -
39M ARG* 3.6 22.2 + - + +
40M GLU* 3.3 51.2 + - - +
42M VAL* 4.1 5.5 - - - +
45M GLN* 5.5 1.2 - - - +
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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