Contacts of the helix formed by residues 35 - 44 (chain Y) 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 Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33Y ILE* 3.5 3.4 + - - +
34Y ASP* 1.3 71.8 - - - +
36Y SER* 1.3 53.6 + - - +
38Y SER* 2.9 7.7 + - - -
39Y ILE* 2.5 43.7 + - + +
67Y MET* 5.2 1.6 - - + -
83Y TYR* 4.1 13.2 - - + -
84Y VAL 2.7 32.2 + - - +
85Y PHE* 3.5 32.5 - - + -
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Residues in contact with SER 36 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34Y ASP* 3.2 6.9 + - - -
35Y ALA* 1.3 82.4 - - - +
37Y MET* 1.3 63.8 + - - +
39Y ILE* 3.0 8.4 + - - +
40Y TYR* 2.9 20.5 + - - +
84Y VAL 3.7 0.7 + - - -
85Y PHE* 4.3 4.8 - - - -
86Y ASP* 2.5 43.8 + - - +
138Y ASN* 5.2 5.0 + - - -
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Residues in contact with MET 37 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34Y ASP* 2.7 23.5 + - - +
36Y SER* 1.3 73.7 - - - +
38Y SER* 1.3 52.6 + - - +
40Y TYR* 3.1 15.8 + - + +
41Y GLN* 2.7 51.1 + - - +
160Y GLU* 5.5 2.5 - - - +
177Y THR* 3.2 12.6 - - + -
178Y GLU* 3.1 42.4 - - + -
179Y ASP* 3.0 38.8 - - - +
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Residues in contact with SER 38 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33Y ILE* 3.2 23.6 - - - +
34Y ASP* 2.6 27.7 + - - +
35Y ALA* 3.1 9.0 - - - -
37Y MET* 1.3 73.8 - - - +
39Y ILE* 1.3 65.3 + - - +
41Y GLN* 2.8 20.6 + - - +
42Y PHE* 2.8 33.1 - - - -
67Y MET* 6.4 0.4 - - - -
83Y TYR* 4.6 7.2 - - - -
176Y ALA 5.0 0.2 + - - -
195Y THR* 4.2 10.5 + - - +
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Residues in contact with ILE 39 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35Y ALA* 2.5 30.2 + - + +
36Y SER* 3.5 4.3 - - - +
38Y SER* 1.3 74.0 - - - +
40Y TYR* 1.3 64.4 + - - +
42Y PHE* 3.4 18.9 + - - +
43Y LEU* 3.5 19.0 + - + +
63Y HIS* 4.0 26.7 - - + +
67Y MET* 4.8 8.3 - - + -
85Y PHE* 3.5 22.4 - - + -
137Y HIS* 4.5 9.4 - - + +
138Y ASN* 3.4 39.0 - - - +
141Y CYS* 4.0 13.9 - - + -
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Residues in contact with TYR 40 (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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36Y SER 2.9 13.0 + - - +
37Y MET* 3.2 18.8 - - + +
39Y ILE* 1.3 75.3 - - - +
41Y GLN* 1.3 81.2 + - - +
43Y LEU* 2.8 31.6 + - + +
44Y ILE* 3.1 35.1 + - + +
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Residues in contact with GLN 41 (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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37Y MET* 2.7 42.0 + - - +
38Y SER* 2.8 14.1 + - - +
40Y TYR* 1.3 85.4 - - - +
42Y PHE* 1.3 68.8 + - + +
44Y ILE* 3.4 20.7 - - - +
178Y GLU* 3.8 20.1 - - + +
195Y THR* 5.1 13.1 + - - +
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Residues in contact with PHE 42 (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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38Y SER* 2.8 42.6 - - - -
39Y ILE* 3.4 16.4 - - - +
40Y TYR 3.1 0.4 - - - -
41Y GLN* 1.3 77.4 - - + +
43Y LEU* 1.3 68.0 + - - +
44Y ILE 4.3 2.8 - - - +
62Y SER* 3.6 36.8 + - - +
63Y HIS* 4.5 4.7 - - - -
66Y GLY* 3.7 17.9 - - - -
67Y MET* 4.2 20.4 - - + -
70Y ARG* 3.4 46.0 - - + +
83Y TYR* 5.0 5.2 - - - -
195Y THR* 4.1 19.5 - - + -
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Residues in contact with LEU 43 (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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39Y ILE* 3.5 17.2 + - + +
40Y TYR* 2.8 21.2 + - + +
42Y PHE* 1.3 82.4 - - - +
44Y ILE* 1.3 62.6 + - + +
60Y THR* 5.1 15.5 - - + -
62Y SER* 4.5 8.3 + - - -
63Y HIS* 4.3 26.0 - - + +
137Y HIS* 3.9 31.0 - - + +
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Residues in contact with ILE 44 (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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40Y TYR* 3.1 37.1 + - + +
41Y GLN* 3.4 17.3 - - - +
42Y PHE 4.3 2.0 - - - +
43Y LEU* 1.3 84.5 - - + +
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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