Contacts of the helix formed by residues 37 - 47 (chain C) in PDB entry 4BEJ
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 GLY 37 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34C GLN 4.0 6.7 + - - -
35C SER 3.2 6.7 - - - -
36C SER* 1.3 78.7 + - - +
38C LYS* 1.3 63.7 + - - +
39C SER* 3.2 4.7 - - - -
40C SER* 2.5 32.1 + - - -
41C VAL* 3.4 8.4 + - - +
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Residues in contact with LYS 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C VAL* 4.5 7.3 - - + +
31C VAL 4.5 1.8 - - - -
32C GLY* 3.4 40.2 - - - +
33C THR 4.4 4.7 + - - +
34C GLN* 4.4 11.1 + - - +
36C SER* 3.4 10.6 - - - +
37C GLY* 1.3 73.7 - - - +
39C SER* 1.3 73.7 + - - +
40C SER 3.2 0.2 - - - -
41C VAL* 3.3 7.3 + - - +
42C LEU* 3.3 25.2 + - - +
146C ASP* 3.3 25.2 + - - +
147C LEU 3.0 27.0 + - - +
148C PRO* 4.7 0.6 - - - +
149C GLY* 3.6 14.6 - - - +
184C VAL* 4.0 26.5 - - + -
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Residues in contact with SER 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C GLN* 5.4 6.1 + - - -
37C GLY* 5.0 2.0 - - - -
38C LYS* 1.3 89.2 + - - +
40C SER* 1.3 61.9 + - - +
42C LEU* 3.3 4.9 + - - +
43C GLU* 3.0 34.1 + - - +
51C LEU* 4.3 26.0 - - - +
52C PRO 5.4 3.8 + - - -
146C ASP* 5.5 0.7 + - - -
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Residues in contact with SER 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C GLY* 2.5 27.4 + - - -
39C SER* 1.3 81.0 - - - +
41C VAL* 1.3 57.9 + - - +
43C GLU* 3.3 13.0 + - - +
44C SER* 2.8 36.8 + - - -
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Residues in contact with VAL 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C VAL* 5.9 0.4 - - + -
37C GLY 3.5 14.1 - - - +
38C LYS* 3.3 15.7 - - + +
40C SER* 1.3 77.3 + - - +
42C LEU* 1.3 69.7 + - + +
44C SER* 3.3 6.8 + - - -
45C LEU* 3.2 32.8 + - + +
182C LEU* 5.1 13.9 - - + -
184C VAL* 4.1 20.4 - - + -
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Residues in contact with LEU 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C VAL* 4.2 18.2 - - + -
38C LYS 3.3 14.7 + - - +
39C SER* 3.3 6.3 + - - +
41C VAL* 1.3 83.5 - - + +
43C GLU* 1.3 62.3 + - - +
45C LEU* 3.2 18.1 + - + +
46C VAL* 3.3 16.2 + - - +
51C LEU* 3.7 20.6 - - + -
63C LEU* 5.2 1.3 - - + -
65C LEU* 4.3 22.2 - - + +
144C LEU* 3.7 32.3 - - + -
146C ASP* 3.4 42.2 - - + +
182C LEU* 5.6 0.2 - - + -
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Residues in contact with GLU 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C SER* 3.0 24.5 + - - +
40C SER* 3.7 11.9 - - - +
42C LEU* 1.3 79.3 - - - +
44C SER* 1.3 57.5 + - - +
46C VAL* 3.2 9.0 - - - +
47C GLY* 3.0 23.4 + - - -
48C ARG 3.5 18.4 + - - +
49C ASP* 3.5 21.0 - - - +
50C LEU 3.5 6.4 + - - -
51C LEU* 3.2 48.7 + - + +
53C ARG* 5.4 6.6 + - - -
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Residues in contact with SER 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C SER* 2.8 25.7 + - - -
41C VAL* 3.8 7.2 - - - -
42C LEU 3.2 0.6 - - - -
43C GLU* 1.3 75.5 - - - +
45C LEU* 1.3 64.7 + - - +
47C GLY* 3.9 7.7 + - - +
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Residues in contact with LEU 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C VAL* 3.2 23.9 + - + +
42C LEU* 3.2 14.7 + - + +
44C SER* 1.3 79.0 - - - +
46C VAL* 1.3 62.7 + - - +
47C GLY 3.5 0.2 + - - -
65C LEU* 6.1 1.3 - - + -
67C LEU* 4.0 16.5 - - + +
138C ASN 4.5 2.9 - - - +
139C VAL* 3.7 15.6 - - - +
140C VAL* 5.4 4.4 + - + -
142C LEU* 3.9 20.2 - - + -
144C LEU* 3.5 31.9 - - + -
182C LEU* 6.0 0.7 - - + -
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Residues in contact with VAL 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C LEU 3.3 12.3 - - - +
43C GLU* 3.2 15.3 - - - +
45C LEU* 1.3 80.0 - - - +
47C GLY* 1.3 61.6 + - - +
48C ARG* 3.5 21.4 - - + +
50C LEU* 3.6 28.3 - - + -
51C LEU* 5.8 0.4 - - + -
65C LEU* 5.2 4.3 - - + -
67C LEU* 4.0 15.2 - - + +
89C GLU* 4.4 10.2 - - - +
104C PHE* 4.5 5.2 - - + -
134C ILE* 3.8 26.0 - - + -
136C SER* 4.7 0.8 + - - -
138C ASN* 4.9 3.3 - - - +
139C VAL* 3.2 22.9 - - + +
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Residues in contact with GLY 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C GLU 3.0 11.5 + - - -
44C SER* 3.9 8.5 + - - -
45C LEU 3.3 3.0 - - - -
46C VAL* 1.3 75.9 - - - +
48C ARG* 1.3 75.2 + - - +
89C GLU* 5.3 1.3 - - - +
138C ASN* 6.0 2.7 - - - -
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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