Contacts of the helix formed by residues 21 - 31 (chain M) in PDB entry 3Q2K
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 ILE 21 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287D ARG* 3.9 6.3 - - - +
20M ARG* 1.3 77.2 - - - +
22M SER* 1.3 68.3 + - - +
23M LYS 3.1 1.1 - - - -
24M ASN* 3.1 28.5 + - + +
25M HIS* 3.4 13.8 - - + -
79M ALA* 3.6 20.4 - - + -
102M GLU* 3.6 16.4 - - - +
301M HIS* 3.6 20.0 - - + +
500M NAI 2.9 75.0 + - + +
550M HP7 5.2 1.1 - - - +
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Residues in contact with SER 22 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15M LEU* 3.6 18.4 - - - -
17M GLY 3.3 24.2 - - - -
18M CYS* 3.2 13.6 + - - +
19M GLY 2.3 24.8 + - - -
21M ILE* 1.3 82.7 - - - +
23M LYS* 1.3 70.6 + - - +
25M HIS* 2.8 16.9 + - - +
26M ILE* 2.9 24.1 + - - +
79M ALA* 4.7 1.3 - - - -
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Residues in contact with LYS 23 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288D GLU* 3.1 51.9 + - + +
291D TYR* 5.1 3.8 - - - +
292D GLU* 6.3 0.2 - - - -
18M CYS 5.6 2.8 + - - -
19M GLY 5.3 3.3 + - - +
20M ARG* 3.7 15.1 + - - +
21M ILE 3.1 0.2 - - - -
22M SER* 1.3 86.4 + - - +
24M ASN* 1.3 63.2 + - - +
26M ILE* 3.4 11.1 + - + +
27M GLY* 2.8 27.0 + - - -
51M ALA* 5.9 4.6 - - - +
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Residues in contact with ASN 24 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287D ARG* 1.9 49.7 + - - +
288D GLU* 4.8 6.1 - - - +
291D TYR* 3.6 30.1 + - + -
20M ARG 4.9 2.6 + - - -
21M ILE* 3.1 16.3 + - + +
23M LYS* 1.3 83.0 - - - +
25M HIS* 1.3 58.6 + - - +
26M ILE 3.3 0.2 - - - -
28M ALA* 2.8 28.4 + - - +
298M GLY 3.1 7.4 - - - +
301M HIS* 3.6 23.1 + - + +
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Residues in contact with HIS 25 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15M LEU* 4.6 7.6 - - + -
21M ILE* 3.4 32.5 + - + -
22M SER* 2.8 9.9 + - - +
24M ASN* 1.3 76.7 - - - +
26M ILE* 1.3 59.1 + - - +
28M ALA* 3.7 4.4 - - - +
29M ILE* 2.8 43.3 + - + +
77M VAL* 3.4 20.1 - - + +
79M ALA* 4.6 5.2 - - + -
100M VAL* 5.1 0.2 - - + -
102M GLU* 2.6 35.0 + - + +
129M VAL* 4.1 14.8 - - + -
301M HIS* 3.4 18.3 + + - -
305M TYR* 2.6 33.2 + + - +
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Residues in contact with ILE 26 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15M LEU* 3.7 22.7 - - + -
18M CYS* 6.0 0.4 - - - -
22M SER* 2.9 26.7 + - - +
23M LYS* 3.6 10.5 - - + +
25M HIS* 1.3 74.7 - - - +
27M GLY* 1.3 66.8 + - - +
29M ILE* 3.3 7.8 + - - +
30M ALA* 3.0 24.2 + - + +
38M LEU* 3.8 15.0 - - + -
41M ILE* 5.8 1.3 - - + -
52M ALA* 5.2 10.8 - - + -
55M ALA* 5.8 3.1 - - + +
56M THR* 3.9 30.1 - - + -
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Residues in contact with GLY 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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291D TYR* 3.6 27.9 - - - -
295D SER* 6.0 0.3 - - - -
23M LYS 2.8 16.8 + - - -
24M ASN 3.9 0.2 - - - -
26M ILE* 1.3 79.4 - - - +
28M ALA* 1.3 65.5 + - - +
30M ALA* 3.2 18.6 - - - +
31M GLN* 3.3 7.4 + - - +
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Residues in contact with ALA 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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291D TYR* 3.5 3.2 - - - -
24M ASN 2.8 22.6 + - - +
25M HIS 3.7 3.4 - - - +
27M GLY* 1.3 71.4 - - - +
29M ILE* 1.3 64.1 + - - +
31M GLN* 3.4 8.0 + - - +
32M HIS* 3.3 21.7 - - - -
301M HIS* 3.7 12.3 - - + -
302M PRO* 3.8 21.3 - - + -
305M TYR* 3.4 29.8 - - + -
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Residues in contact with ILE 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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13M PHE* 4.0 30.5 - - + -
15M LEU* 5.9 1.8 - - + -
25M HIS* 2.8 26.1 + - + +
26M ILE* 3.7 6.7 - - + +
28M ALA* 1.3 70.3 - - - +
30M ALA* 1.3 71.3 + - - +
32M HIS* 3.1 20.7 + - - +
33M GLY* 3.7 1.7 + - - -
36M ALA* 4.2 8.8 - - + +
37M GLU* 3.9 8.1 - - - -
38M LEU* 3.7 41.3 - - + +
77M VAL* 5.1 3.4 - - + -
305M TYR* 4.0 32.7 - - + +
309M ILE* 6.0 0.7 - - - -
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Residues in contact with ALA 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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295D SER* 5.1 13.9 - - - +
26M ILE* 3.0 13.5 + - + +
27M GLY* 3.2 13.2 - - - +
29M ILE* 1.3 69.9 - - - +
31M GLN* 1.3 53.7 - - - +
32M HIS 2.2 21.9 + - - -
33M GLY* 2.3 25.4 + - - -
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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
----------------------------------------------------------
291D TYR* 4.5 12.3 + - - -
294D THR* 5.7 7.8 - - - +
295D SER* 5.3 11.7 - - - -
27M GLY 3.3 4.8 + - - +
28M ALA 3.5 10.3 - - - +
30M ALA* 1.3 75.8 - - - +
32M HIS* 1.3 65.3 + - + +
33M GLY 3.4 2.8 + - - -
34M ASP* 4.7 2.3 - - - +
302M PRO* 3.7 36.4 - - + +
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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