Contacts of the helix formed by residues 49 - 61 (chain H) in PDB entry 1UW9
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 49 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21H ARG* 3.9 20.9 - - - +
47H GLY 3.5 10.5 - - - +
48H VAL* 1.3 89.6 - - + +
50H PRO* 1.3 71.6 - - + +
51H GLU* 3.7 14.4 - - - +
52H GLU* 3.0 15.4 + - + +
53H CYS* 3.0 19.9 + - - +
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Residues in contact with PRO 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42H MET* 3.5 16.0 - - + +
44H PRO* 4.4 3.6 - - + -
48H VAL 3.5 3.8 - - - +
49H PRO* 1.3 84.2 - - + +
51H GLU* 1.3 71.7 + - - +
53H CYS* 4.3 3.8 - - + -
54H GLY 2.8 25.3 + - - -
87H ILE* 3.5 11.9 - - + +
97H TYR* 3.8 51.8 - - + +
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Residues in contact with GLU 51 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H ARG* 3.6 33.0 + - - +
25H TYR* 3.7 44.2 + - + +
49H PRO* 3.7 9.4 - - - +
50H PRO* 1.3 93.4 - - - +
52H GLU* 1.3 55.3 + - - +
54H GLY* 3.6 0.3 + - - -
55H ALA* 2.9 30.1 + - - +
87H ILE* 3.6 12.8 - - + -
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Residues in contact with GLU 52 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19H ASP* 3.4 14.4 - - - +
20H TYR* 2.8 27.4 + - - -
21H ARG* 2.9 42.7 + - - +
48H VAL* 4.5 2.2 - - + -
49H PRO* 3.0 27.2 + - + +
51H GLU* 1.3 74.9 - - - +
53H CYS* 1.3 60.5 + - - +
55H ALA* 3.4 1.2 + - - +
56H ALA* 2.8 28.6 + - - +
1480H EDO 2.8 40.1 + - - +
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Residues in contact with CYS 53 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42H MET* 3.7 28.7 - - + -
44H PRO* 3.9 22.2 - - + -
48H VAL* 4.0 11.6 - - + +
49H PRO 3.0 15.0 + - - +
50H PRO 3.8 2.2 - - - +
52H GLU* 1.3 74.7 - - - +
54H GLY* 1.3 63.8 + - - +
56H ALA* 3.4 7.3 + - - +
57H VAL* 3.1 27.2 + - - +
129H ALA* 4.2 9.6 - - - -
130H LEU* 3.9 26.7 - - - -
1480H EDO 6.1 0.4 - - - -
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Residues in contact with GLY 54 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42H MET* 3.5 15.8 - - - -
50H PRO 2.8 19.9 + - - -
51H GLU 4.0 0.2 - - - -
53H CYS* 1.3 72.6 - - - +
55H ALA* 1.3 56.8 + - - +
57H VAL* 3.3 5.9 + - - +
58H ALA* 2.9 28.8 + - - +
84H CYS* 3.7 23.4 - - - +
99H ALA* 4.3 4.5 - - - -
101H VAL* 4.7 2.1 - - - +
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Residues in contact with ALA 55 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20H TYR* 3.7 6.7 - - - +
21H ARG* 3.4 35.0 - - - +
24H TYR* 3.4 14.4 - - - +
25H TYR* 3.9 11.0 - - + +
51H GLU 2.9 19.8 + - - +
52H GLU 3.6 3.8 - - - +
53H CYS 3.3 0.2 - - - -
54H GLY* 1.3 77.0 - - - +
56H ALA* 1.3 56.3 + - - +
58H ALA* 3.4 0.6 + - - -
59H ALA* 2.8 31.4 + - - +
84H CYS* 4.1 1.8 - - - +
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Residues in contact with ALA 56 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20H TYR* 3.5 33.8 - - + +
52H GLU 2.8 18.0 + - - +
53H CYS* 3.6 9.6 - - - +
54H GLY 3.3 0.2 - - - -
55H ALA* 1.3 73.9 - - - +
57H VAL* 1.3 59.6 + - + +
60H GLU* 2.9 36.8 + - - +
124H VAL* 5.0 0.2 - - - -
127H PHE* 5.1 13.0 - - + -
129H ALA* 5.9 3.8 - - + -
130H LEU* 6.5 0.7 - - + -
1480H EDO 4.9 6.1 - - - -
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Residues in contact with VAL 57 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40H PHE* 3.7 45.1 - - + -
42H MET* 4.7 4.9 - - - -
53H CYS 3.1 15.9 + - - +
54H GLY* 3.6 9.0 - - - +
56H ALA* 1.3 76.0 - - + +
58H ALA* 1.3 54.5 + - - +
61H SER* 2.7 34.7 + - - +
99H ALA* 6.1 1.6 - - + -
101H VAL* 4.6 3.4 - - + -
124H VAL* 3.4 18.6 - - + +
130H LEU* 3.9 26.9 - - + -
133H LEU* 4.3 13.2 - - + -
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Residues in contact with ALA 58 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24H TYR* 4.0 5.8 - - + +
54H GLY 2.9 17.4 + - - +
55H ALA 3.7 4.3 - - - +
57H VAL* 1.3 77.2 - - - +
59H ALA* 1.3 53.8 + - - +
61H SER* 3.4 9.5 + - - -
62H SER* 2.6 31.6 + - - -
82H GLY* 4.0 11.9 - - - +
84H CYS* 3.6 27.4 - - + +
101H VAL* 3.8 19.9 - - + +
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Residues in contact with ALA 59 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20H TYR* 3.4 31.2 - - + -
24H TYR* 3.4 31.8 - - + -
55H ALA 2.8 20.5 + - - +
56H ALA 3.7 0.9 - - - +
58H ALA* 1.3 73.6 - - - +
60H GLU* 1.3 58.2 + - - +
62H SER 3.1 13.2 + - - -
63H THR 3.1 1.2 + - - -
64H GLY* 2.8 26.2 + - - -
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Residues in contact with GLU 60 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20H TYR* 2.7 30.6 + - + +
56H ALA 2.9 19.2 + - - +
59H ALA* 1.3 74.2 - - - +
61H SER* 1.3 57.3 + - - +
62H SER 3.4 0.4 - - - -
64H GLY 3.4 18.2 - - - +
65H THR* 3.2 11.0 - - - -
66H TRP 3.5 0.3 + - - -
119H SER 4.8 0.7 - - - +
123H ASN* 4.5 11.1 + - + +
124H VAL* 3.8 12.4 - - + +
127H PHE* 3.2 36.4 - - + -
177R LYS* 3.6 20.4 + - - -
204R GLU* 5.0 0.2 - - - +
334R LYS* 3.1 29.0 + - - -
1476R CAP 3.4 10.9 + - - -
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Residues in contact with SER 61 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57H VAL 2.7 20.9 + - - -
58H ALA 3.4 3.3 + - - -
59H ALA 3.2 0.2 - - - -
60H GLU* 1.3 78.6 - - - +
62H SER* 1.3 58.6 + - - +
103H TYR* 2.6 43.0 + - - -
107H LEU* 5.1 0.5 - - - +
119H SER* 3.1 42.2 - - - -
120H ILE 4.2 5.6 - - - -
124H VAL* 4.1 9.2 - - - -
177R LYS* 4.8 0.7 - - - +
205R ASN* 4.6 5.4 - - - -
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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