Contacts of the helix formed by residues 34 - 46 (chain R) 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 TYR 34 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25Q PHE* 3.6 37.0 - + - -
26Q PRO* 3.7 15.9 - - + -
29Q ARG* 4.2 22.5 - - - +
30Q VAL* 3.9 20.5 - - + +
33Q LEU* 4.3 11.7 - - + +
55Q LEU* 4.7 3.2 - - + +
33R SER* 1.3 80.3 + - - +
35R SER* 1.3 62.3 + - - +
36R ILE 3.7 1.3 - - - -
37R TYR* 3.6 21.1 - + + -
38R VAL* 3.1 26.2 + - + +
56R MET* 3.3 11.3 - - + +
60R ASN* 3.1 24.9 - - + +
63R VAL* 3.7 23.6 - - + +
64R ASN* 4.4 13.5 - - - -
67R PHE* 5.6 3.6 - - - -
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Residues in contact with SER 35 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-121I C 3.4 22.7 + - - -
33R SER* 3.3 13.7 + - - -
34R TYR* 1.3 77.8 - - - +
36R ILE* 1.3 74.5 + - - +
38R VAL* 3.8 1.7 - - - +
39R TYR* 2.9 48.0 + - - -
56R MET* 3.7 16.8 - - - -
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Residues in contact with ILE 36 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-123I G 5.4 0.7 - - + -
-122I G 3.3 47.6 - - + +
-121I C 3.5 40.6 - - + +
35R SER* 1.3 87.2 + - - +
37R TYR* 1.3 67.1 + - + +
39R TYR* 3.4 21.7 - - + +
40R LYS* 2.9 50.2 + - - +
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Residues in contact with TYR 37 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-122I G 2.4 51.3 + - - -
-121I C 3.9 8.1 - - - -
18Q SER* 5.5 0.7 - - - -
24Q GLN* 3.2 26.7 - - - +
25Q PHE* 4.7 7.6 - - + -
26Q PRO* 3.6 31.2 - - + +
29Q ARG* 2.4 47.8 + - - -
33R SER 3.7 2.2 - - - -
34R TYR* 3.6 28.3 - + + +
35R SER 3.2 1.0 - - - -
36R ILE* 1.3 77.5 - - + +
38R VAL* 1.3 59.8 + - - +
40R LYS* 3.3 9.6 + - + +
41R VAL* 2.9 34.9 + - - +
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Residues in contact with VAL 38 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25Q PHE* 4.8 14.1 - - + -
59Q THR* 5.0 5.8 - - + -
63Q LEU* 4.2 8.0 - - + +
34R TYR* 3.1 28.9 + - + +
35R SER 3.8 0.4 - - - +
37R TYR* 1.3 72.4 - - - +
39R TYR* 1.3 60.0 + - + +
41R VAL* 3.8 6.6 - - - +
42R LEU* 2.9 29.1 + - - +
51R ILE* 3.8 20.0 - - + -
56R MET* 3.7 29.4 - - + -
59R MET* 4.1 22.2 - - + -
63R VAL* 4.8 6.3 - - + -
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Residues in contact with TYR 39 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116J C 5.4 1.2 - - - +
117J A 3.4 46.0 + + + -
118J C 5.7 11.0 - + - +
35R SER* 2.9 33.8 + - - -
36R ILE* 3.4 25.4 - - + +
38R VAL* 1.3 78.0 - - - +
40R LYS* 1.3 58.3 + - + +
42R LEU* 3.4 5.3 + - - +
43R LYS* 2.9 37.9 + - + +
51R ILE* 3.6 24.2 + - + -
56R MET* 4.1 21.1 - - + +
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Residues in contact with LYS 40 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-123I G 5.1 2.2 - - - -
-122I G 3.2 25.3 + - - -
24Q GLN* 3.3 29.6 - - + +
36R ILE* 2.9 39.9 + - - +
37R TYR* 3.7 11.6 - - + +
39R TYR* 1.3 73.5 - - + +
41R VAL* 1.3 60.8 + - - +
43R LYS* 3.7 6.4 - - - +
44R GLN* 2.9 34.8 + - - +
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Residues in contact with VAL 41 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24Q GLN* 4.2 11.9 - - + -
25Q PHE* 3.9 23.1 - - + -
56Q GLU* 4.2 16.8 - - + -
59Q THR* 3.8 16.8 - - - +
60Q ALA* 4.1 19.7 - - + +
63Q LEU* 3.8 17.7 - - + -
37R TYR 2.9 20.4 + - - +
38R VAL* 3.8 5.8 - - - +
40R LYS* 1.3 78.1 - - - +
42R LEU* 1.3 57.7 + - - +
44R GLN* 3.2 10.1 + - - +
45R VAL* 3.0 30.2 + - + +
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Residues in contact with LEU 42 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63Q LEU* 3.8 37.7 - - + +
67Q GLY 5.7 0.2 - - - +
78Q ILE* 3.8 12.1 - - + -
38R VAL* 2.9 18.3 + - + +
39R TYR* 3.8 4.7 - - - +
41R VAL* 1.3 78.4 - - - +
43R LYS* 1.3 55.0 + - - +
45R VAL* 3.5 7.6 - - + +
46R HIS* 2.6 49.8 + - + +
49R THR* 3.4 26.9 - - + +
50R GLY* 4.0 6.3 - - - +
51R ILE* 3.7 36.1 - - + -
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Residues in contact with LYS 43 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117J A 3.8 18.3 + - - -
118J C 3.6 31.7 + - - +
39R TYR* 2.9 25.0 + - + +
40R LYS* 3.9 6.1 - - - +
42R LEU* 1.3 77.1 - - - +
44R GLN* 1.3 61.2 + - - +
46R HIS 3.9 3.1 - - - +
47R PRO* 4.0 44.8 - - + +
49R THR 4.2 15.9 - - - -
50R GLY* 5.8 0.2 - - - -
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Residues in contact with GLN 44 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24Q GLN* 3.3 45.0 - - - +
56Q GLU* 3.8 9.3 + - - +
40R LYS 2.9 18.5 + - - +
41R VAL* 3.2 12.2 + - - +
43R LYS* 1.3 79.0 - - - +
45R VAL* 1.3 62.9 + - + +
47R PRO* 5.3 1.7 - - - +
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Residues in contact with VAL 45 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60Q ALA* 4.0 31.9 - - + +
63Q LEU* 3.8 23.8 - - + -
64Q GLU* 4.8 10.3 - - + +
41R VAL* 3.0 19.8 + - + +
42R LEU* 3.5 12.6 - - + +
44R GLN* 1.3 84.5 - - + +
46R HIS* 1.3 86.9 + - + +
47R PRO* 4.3 3.6 - - - +
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Residues in contact with HIS 46 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63Q LEU 3.6 9.5 + - - -
64Q GLU* 3.3 46.7 + - - -
67Q GLY* 3.5 29.6 - - - -
68Q ASN* 3.9 4.4 + - - -
42R LEU* 2.6 31.0 + - + +
43R LYS* 3.9 2.5 - - - +
44R GLN 3.6 1.0 - - - -
45R VAL* 1.3 91.1 + - - +
47R PRO* 1.3 69.9 - - + +
48R ASP* 3.3 8.5 + - - -
49R THR* 3.6 34.5 + - - +
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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
------------------------------------------------------------
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