Contacts of the helix formed by residues 35 - 44 (chain Z) in PDB entry 1UL1
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 ALA 35 (chain Z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33Z ILE 3.1 5.3 + - - -
34Z ASP* 1.3 69.9 - - - +
36Z SER* 1.3 60.3 + - - +
38Z SER* 3.7 2.3 - - - -
39Z ILE* 3.2 24.3 + - - +
67Z MET* 5.2 3.7 - - + +
83Z TYR* 4.2 14.6 - - + -
84Z VAL 2.8 35.5 + - - +
85Z PHE* 3.1 41.7 - - + +
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Residues in contact with SER 36 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34Z ASP* 3.1 2.3 + - - -
35Z ALA* 1.3 73.7 - - - +
37Z MET* 1.3 57.2 + - - +
38Z SER 2.6 16.6 + - - -
39Z ILE* 3.1 4.5 + - - -
40Z TYR* 3.0 25.8 + - - +
84Z VAL 4.0 0.4 + - - -
85Z PHE* 4.1 3.4 - - - +
86Z ASP* 2.6 52.3 + - - +
134Z THR* 5.4 9.9 - - - +
138Z ASN* 5.0 7.6 + - - +
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Residues in contact with MET 37 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34Z ASP* 3.1 28.1 + - + +
36Z SER* 1.3 77.4 - - - +
38Z SER* 1.3 56.1 + - - +
40Z TYR* 3.3 40.6 - - + -
41Z GLN* 3.0 48.2 + - - +
177Z THR* 3.5 21.8 - - + -
178Z GLU* 4.2 7.1 - - + +
179Z ASP* 4.1 26.2 - - + +
195Z THR* 5.3 0.3 + - - -
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Residues in contact with SER 38 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33Z ILE* 3.3 9.9 - - - +
34Z ASP* 2.8 20.9 + - - +
35Z ALA* 3.7 5.4 - - - -
36Z SER 2.6 5.9 + - - -
37Z MET* 1.3 72.3 - - - +
39Z ILE* 1.3 58.0 + - - -
40Z TYR 3.1 1.3 - - - -
41Z GLN* 2.7 27.1 + - - +
42Z PHE* 2.8 34.9 + - - -
67Z MET* 5.9 0.9 - - - -
83Z TYR* 4.9 4.5 - - - -
176Z ALA 5.0 0.3 + - - -
195Z THR* 3.2 29.4 - - - +
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Residues in contact with ILE 39 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35Z ALA 3.2 13.7 + - - +
36Z SER* 3.1 4.1 + - - +
38Z SER* 1.3 78.9 - - - +
40Z TYR* 1.3 64.5 + - - +
42Z PHE* 3.2 15.7 + - - +
43Z LEU* 3.2 28.1 + - + +
63Z HIS* 5.1 7.7 - - + -
67Z MET* 5.5 3.3 - - + +
85Z PHE* 5.9 3.6 - - + -
134Z THR* 6.0 5.4 - - + +
137Z HIS* 5.2 9.2 - - + +
138Z ASN* 5.9 5.6 - - - +
141Z CYS* 5.0 16.4 - - - -
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Residues in contact with TYR 40 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36Z SER 3.0 17.0 + - - +
37Z MET* 3.3 33.0 - - + +
39Z ILE* 1.3 78.3 - - - +
41Z GLN* 1.3 69.6 + - - +
43Z LEU* 3.2 8.9 + - + +
44Z ILE* 3.1 29.1 + - + +
128Z LYS 5.2 4.0 + - - -
131Z VAL 3.6 25.6 - - - -
132Z LYS* 4.4 28.7 - - + +
134Z THR* 4.4 17.5 - - + +
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Residues in contact with GLN 41 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37Z MET* 3.0 27.5 + - - +
38Z SER* 2.7 20.6 + - - +
40Z TYR* 1.3 81.6 - - - +
42Z PHE* 1.3 63.7 + - + +
44Z ILE* 3.1 24.5 + - - +
45Z ALA* 3.7 4.2 - - - +
178Z GLU* 3.1 35.3 + - + +
195Z THR* 4.4 15.2 + - - +
196Z ALA* 6.5 0.2 - - - -
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Residues in contact with PHE 42 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38Z SER* 2.8 46.3 + - - -
39Z ILE* 3.2 14.3 + - - +
41Z GLN* 1.3 74.6 - - + +
43Z LEU* 1.3 62.6 + - - +
45Z ALA* 3.2 18.8 - - - +
46Z VAL* 4.0 3.5 + - - +
62Z SER* 4.1 11.9 - - - +
63Z HIS* 4.5 18.8 - - - +
66Z GLY* 3.9 16.6 - - - -
67Z MET* 4.4 23.8 - - + -
70Z ARG* 3.0 52.0 - - + +
83Z TYR* 5.3 4.0 - + - -
195Z THR* 3.4 27.8 - - - -
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Residues in contact with LEU 43 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39Z ILE* 3.2 18.9 + - + +
40Z TYR* 3.7 8.5 - - - +
42Z PHE* 1.3 72.9 - - - +
44Z ILE* 1.3 53.7 + - - +
45Z ALA 2.7 17.9 + - - -
46Z VAL* 3.5 14.9 + - - +
47Z ARG* 3.7 10.2 + - - +
60Z THR* 4.6 11.0 - - + -
62Z SER* 3.5 25.8 - - - +
63Z HIS* 3.7 20.9 - - + +
131Z VAL* 3.8 17.4 - - + +
133Z VAL* 3.5 35.2 - - + +
134Z THR* 4.9 1.6 - - - -
137Z HIS* 3.6 21.8 - - + +
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Residues in contact with ILE 44 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40Z TYR* 3.1 33.3 + - + +
41Z GLN* 3.1 11.6 + - - +
43Z LEU* 1.3 73.4 - - - +
45Z ALA* 1.3 59.6 + - - +
47Z ARG* 4.5 5.6 - - - -
128Z LYS* 4.6 25.9 + - + +
131Z VAL* 4.0 16.5 - - + +
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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