Contacts of the helix formed by residues 26 - 36 (chain Y) in PDB entry 6L49
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 PRO 26 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218I G 5.6 0.4 - - - +
-214J G 5.9 3.8 - - - -
-213J A 5.7 0.4 - - - +
18Y SER* 3.4 10.1 - - - +
25Y PHE* 1.3 82.4 - - + +
27Y VAL* 1.3 65.1 + - - +
28Y GLY 4.7 0.7 - - - +
29Y ARG* 3.8 29.2 - - + +
30Y VAL* 3.3 23.8 + - - +
34Z TYR* 3.7 16.2 - - + -
37Z TYR* 3.6 52.5 - - + +
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Residues in contact with VAL 27 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-213J A 4.9 0.4 + - - -
17Y ARG* 3.4 47.3 - - + +
18Y SER* 3.7 6.0 + - - +
21Y ALA* 3.8 15.3 - - + -
23Y LEU* 5.1 2.0 - - + -
25Y PHE 3.8 11.2 - - - +
26Y PRO* 1.3 71.0 - - - +
28Y GLY* 1.3 60.3 + - - +
30Y VAL* 3.4 6.8 + - - +
31Y HIS* 2.9 27.6 + - + +
45Y ALA 5.6 0.2 - - - +
48Y PRO* 3.9 4.8 - - + +
49Y VAL* 3.8 34.5 - - + +
52Y ALA* 4.8 11.0 - - + -
118Z TYR* 4.9 2.9 - - + -
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Residues in contact with GLY 28 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-214J G 3.9 15.6 + - - -
-213J A 3.3 29.4 + - - -
17Y ARG* 3.5 14.6 + - - +
26Y PRO* 3.3 0.8 - - - +
27Y VAL* 1.3 79.9 - - - +
29Y ARG* 1.3 55.1 + - - +
31Y HIS* 3.6 1.4 - - - +
32Y ARG* 2.9 29.8 + - - +
35Y ARG* 5.0 0.7 + - - -
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Residues in contact with ARG 29 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218I G 3.2 21.8 + - - -
219I C 2.5 24.0 + - - -
-214J G 3.3 25.8 + - - +
26Y PRO* 3.5 26.7 + - + +
27Y VAL 3.3 0.4 - - - -
28Y GLY* 1.3 75.6 - - - +
30Y VAL* 1.3 59.8 + - - +
32Y ARG* 3.4 15.7 + - - +
33Y LEU* 2.9 39.1 + - + +
32Z GLU* 3.1 31.8 + - - -
33Z SER 2.8 20.8 + - - +
34Z TYR* 4.2 19.3 - - - +
37Z TYR* 3.0 31.3 + - - -
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Residues in contact with VAL 30 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25Y PHE* 5.6 0.9 - - + -
26Y PRO 3.3 15.9 + - - +
27Y VAL 3.4 3.0 + - - +
28Y GLY 3.4 0.2 - - - -
29Y ARG* 1.3 76.2 - - - +
31Y HIS* 1.3 58.4 + - - +
33Y LEU* 3.4 7.0 + - + +
34Y LEU* 2.9 30.0 + - + +
48Y PRO* 3.8 32.5 - - + +
51Y LEU* 3.9 13.9 - - + -
52Y ALA* 4.6 12.6 - - + +
55Y LEU* 5.1 8.1 - - + -
34Z TYR* 4.0 19.1 - - + +
67Z PHE* 3.7 25.8 - - + -
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Residues in contact with HIS 31 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208I T 5.6 0.9 - - + -
209I A 3.7 20.4 + - - -
17Y ARG* 3.3 38.6 + - - +
27Y VAL* 2.9 19.0 + - + +
28Y GLY 3.6 5.2 - - - +
30Y VAL* 1.3 77.7 - - - +
32Y ARG* 1.3 57.0 + - - +
34Y LEU* 3.5 1.7 + - - +
35Y ARG* 2.9 66.9 + - + +
43Y VAL* 4.3 17.7 - - + +
44Y GLY 4.7 4.5 - - - -
45Y ALA* 5.5 3.8 - - - -
48Y PRO* 3.6 23.8 - - + +
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Residues in contact with ARG 32 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-215J G 3.5 29.7 - - - -
-214J G 3.3 16.8 - - - +
28Y GLY 2.9 17.4 + - - +
29Y ARG* 3.6 18.3 + - - +
31Y HIS* 1.3 75.7 - - - +
33Y LEU* 1.3 73.0 + - - +
35Y ARG* 3.9 20.3 - - - +
36Y LYS* 2.7 51.3 + - + +
32Z GLU* 2.8 31.7 + - - +
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Residues in contact with LEU 33 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29Y ARG* 2.9 26.4 + - + +
30Y VAL* 3.9 2.5 - - + +
32Y ARG* 1.3 95.0 - - - +
34Y LEU* 1.3 60.2 + - - +
36Y LYS 4.6 7.2 - - - +
37Y GLY* 3.3 13.0 - - - -
39Y TYR* 3.2 19.7 - - - -
34Z TYR* 4.3 18.6 - - + +
64Z ASN* 5.1 8.3 - - - +
67Z PHE* 3.6 34.1 - - + -
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Residues in contact with LEU 34 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30Y VAL 2.9 16.2 + - - +
31Y HIS* 4.0 2.7 - - - +
33Y LEU* 1.3 76.6 - - - +
35Y ARG* 1.3 64.4 + - - +
37Y GLY 4.1 0.5 + - - -
39Y TYR* 3.6 41.8 + - + +
40Y SER 5.2 2.4 + - - +
43Y VAL* 3.6 36.4 - - + +
47Y ALA* 4.3 6.5 - - + -
48Y PRO* 3.8 28.3 - - + -
51Y LEU* 3.8 20.2 - - + -
67Z PHE* 3.8 22.0 - - + -
71Z ALA* 4.1 12.1 - - + -
86Z ILE* 5.5 6.5 - - + -
91Z ILE* 5.2 3.1 - - + -
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Residues in contact with ARG 35 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209I A 3.7 45.3 - - - +
210I G 5.6 3.9 + - - +
211I T 5.6 8.3 - - - +
17Y ARG* 4.8 4.9 - - - +
28Y GLY 5.0 0.4 + - - -
31Y HIS* 2.9 44.8 + - + +
32Y ARG* 3.9 24.0 - - - +
34Y LEU* 1.3 79.6 - - - +
36Y LYS* 1.3 88.1 + - + +
37Y GLY 3.2 5.7 + - - -
38Y ASN* 4.0 6.6 + - - -
40Y SER 5.5 2.9 - - - +
43Y VAL* 4.8 4.7 - - + -
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Residues in contact with LYS 36 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210I G 4.9 11.7 - - - -
79V HIS* 5.2 2.5 - - - -
32Y ARG* 2.7 36.8 + - + +
33Y LEU* 3.8 12.2 - - - +
35Y ARG* 1.3 95.8 - - + +
37Y GLY* 1.3 55.9 + - - +
38Y ASN* 3.8 4.5 - - - +
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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