Contacts of the helix formed by residues 36 - 48 (chain Y) in PDB entry 2W4T
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 SER 36 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30Y ASP* 4.5 1.0 + - - -
34Y PHE* 3.6 19.1 - - - -
35Y VAL* 1.3 69.9 - - - +
37Y LYS* 1.3 58.0 + - - +
38Y GLU* 3.5 11.6 + - - +
39Y ASP* 2.2 73.6 + - - +
40Y ILE* 3.1 9.8 + - - +
60Y LEU* 4.1 3.6 - - - -
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Residues in contact with LYS 37 (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* 1.3 72.7 - - - +
38Y GLU* 1.3 65.4 + - + +
40Y ILE* 3.0 22.9 - - - +
41Y LYS* 3.2 16.6 + - + +
53Y ASP* 2.6 55.3 + - - +
56Y LEU* 2.8 47.7 - - + +
57Y THR* 3.5 8.6 - - + +
60Y LEU* 3.6 9.6 - - + +
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Residues in contact with GLU 38 (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 VAL* 5.0 1.6 - - - -
36Y SER* 2.9 9.8 + - - +
37Y LYS* 1.3 86.4 - - + +
39Y ASP* 1.3 61.3 + - - +
41Y LYS* 4.1 18.5 - - - +
42Y ALA* 2.8 32.6 + - - +
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Residues in contact with ASP 39 (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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27Y ILE* 3.9 13.7 - - + +
28Y ASP* 4.5 0.2 - - - -
29Y VAL* 3.1 15.0 + - - +
30Y ASP* 1.6 34.4 + - - +
34Y PHE* 3.2 16.6 - - - +
35Y VAL* 3.1 8.0 - - - -
36Y SER* 2.2 61.2 + - - +
38Y GLU* 1.3 72.2 - - - +
40Y ILE* 1.3 51.0 + - - +
42Y ALA* 3.2 6.9 - - - +
43Y ILE* 2.7 35.9 - - - +
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Residues in contact with ILE 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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825C GLN* 4.5 5.4 - - - +
829C LEU* 4.6 3.8 - - + +
27Y ILE* 5.7 3.1 - - + -
35Y VAL* 5.3 7.0 - - + -
36Y SER 3.3 16.8 - - - +
37Y LYS 3.0 5.4 - - - +
39Y ASP* 1.3 72.1 - - + +
41Y LYS* 1.3 96.5 + - + +
43Y ILE* 2.5 29.7 - - - +
44Y SER* 3.0 11.8 + - - -
51Y PRO* 4.0 29.6 - - + +
56Y LEU* 2.3 47.1 - - + -
59Y MET* 3.8 22.7 - - + -
60Y LEU* 5.1 7.0 - - + -
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Residues in contact with LYS 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 LYS* 3.2 24.3 + - + +
38Y GLU* 4.1 17.3 - - - +
40Y ILE* 1.3 94.3 - - + +
42Y ALA* 1.3 64.6 + - - +
44Y SER* 2.6 21.1 + - - +
45Y GLU* 3.3 27.0 + - + +
50Y ALA* 4.8 5.7 - - + +
51Y PRO 5.0 11.0 + - - +
52Y ASP* 6.3 0.2 - - - +
53Y ASP 6.2 0.2 - - - +
56Y LEU* 5.3 1.8 - - + -
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Residues in contact with ALA 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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29Y VAL* 3.9 20.2 - - + -
38Y GLU 2.8 23.5 + - - +
39Y ASP 3.2 6.5 - - - +
41Y LYS* 1.3 82.3 - - - +
43Y ILE* 1.3 62.6 - - - +
45Y GLU* 3.4 4.8 + - - +
46Y GLN* 3.3 25.0 + - + +
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Residues in contact with ILE 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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829C LEU* 4.9 11.2 - - + -
833C VAL* 5.3 11.2 - - + -
26Y MET 3.5 13.2 - - - +
27Y ILE* 3.2 25.1 - - + +
29Y VAL* 2.9 32.0 - - + +
39Y ASP 2.7 12.3 - - - +
40Y ILE* 2.5 35.7 - - - +
42Y ALA* 1.3 70.3 - - - +
44Y SER* 1.3 74.7 + - - +
46Y GLN* 3.1 20.3 + - - +
47Y LEU* 3.4 12.1 + - - +
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Residues in contact with SER 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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829C LEU* 4.1 25.1 - - - -
832C LYS* 4.8 2.9 - - - +
40Y ILE 3.0 8.9 + - - -
41Y LYS* 2.6 13.5 + - - -
43Y ILE* 1.3 82.4 - - - +
45Y GLU* 1.3 55.7 + - - +
47Y LEU* 2.7 25.6 + - - +
48Y GLY 2.8 22.2 + - - +
49Y ARG 4.5 0.4 - - - -
50Y ALA* 2.4 41.8 - - - +
51Y PRO* 4.2 5.4 - - - -
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Residues in contact with GLU 45 (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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41Y LYS* 3.3 27.9 + - + +
42Y ALA* 3.6 7.4 - - - +
44Y SER* 1.3 77.9 + - - +
46Y GLN* 1.3 61.1 + - + +
47Y LEU* 2.9 16.0 + - - +
48Y GLY 3.7 4.1 - - - +
49Y ARG* 3.7 5.4 - - - +
50Y ALA* 2.9 34.9 + - + +
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Residues in contact with GLN 46 (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 VAL* 6.4 0.2 - - + -
42Y ALA* 3.3 16.8 + - - +
43Y ILE* 3.1 15.8 + - - +
44Y SER 3.1 0.4 + - - -
45Y GLU* 1.3 76.3 - - + +
47Y LEU* 1.3 67.0 + - + +
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Residues in contact with LEU 47 (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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832C LYS* 2.2 78.7 - - + +
833C VAL* 4.6 7.6 - - + +
43Y ILE 3.4 6.7 + - - +
44Y SER 2.7 5.3 + - - +
45Y GLU 2.9 4.2 - - - +
46Y GLN* 1.3 87.2 - - + +
48Y GLY* 1.3 55.5 + - - -
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Residues in contact with GLY 48 (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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832C LYS* 2.2 25.2 - - - +
44Y SER* 2.8 17.9 + - - +
45Y GLU* 3.7 5.2 + - - -
47Y LEU* 1.3 73.1 - - - +
49Y ARG* 1.3 73.0 + - - +
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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