Contacts of the helix formed by residues 52 - 65 (chain B) in PDB entry 3E4E
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 ASN 52 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49B GLU* 2.9 33.1 + - - +
50B LEU 3.0 0.8 - - - -
51B LYS* 1.3 79.8 - - + +
53B ILE* 1.3 67.4 + - - +
54B PRO* 3.8 11.3 - - - +
55B LYS* 3.0 48.8 + - - +
56B SER* 3.2 9.5 + - - -
476B ILE* 3.7 30.5 - - - +
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Residues in contact with ILE 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B LEU* 3.8 36.1 - - + -
49B GLU 3.8 7.4 - - - +
50B LEU* 4.2 24.8 + - + +
52B ASN* 1.3 73.0 - - - +
54B PRO* 1.4 65.0 - - + +
56B SER* 2.7 27.6 + - - -
57B PHE* 2.9 46.9 + - + -
216B GLN* 3.8 26.5 - - + +
366B SER* 4.4 5.4 - - - +
476B ILE 4.6 2.7 + - - +
477B GLY* 5.7 0.9 - - - -
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Residues in contact with PRO 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ASN* 3.5 7.2 - - - +
53B ILE* 1.4 96.6 - - + +
55B LYS* 1.3 61.3 + - - +
57B PHE* 3.4 11.8 + - + +
58B THR* 3.1 27.3 + - - -
365B PRO* 3.9 20.6 - - + -
366B SER* 3.9 10.1 - - - +
394B ASP* 3.4 24.5 - - - +
476B ILE* 3.6 29.2 - - + +
477B GLY 5.1 2.5 - - - +
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Residues in contact with LYS 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B GLU* 3.5 28.9 + - - +
52B ASN* 3.0 37.8 + - - +
54B PRO* 1.3 75.6 - - - +
56B SER* 1.3 57.3 + - - +
58B THR* 3.7 7.3 + - - +
59B ARG* 3.2 26.9 + - + +
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Residues in contact with SER 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B GLN 3.7 15.3 + - - -
48B LEU* 3.6 16.1 - - - -
49B GLU* 2.9 31.7 + - - +
52B ASN 3.2 8.1 + - - -
53B ILE* 2.7 13.1 + - - -
55B LYS* 1.3 77.0 - - - +
57B PHE* 1.3 50.9 + - - -
59B ARG* 3.1 11.4 + - - +
60B LEU* 2.8 40.7 + - - +
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Residues in contact with PHE 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 4.4 8.3 - - + -
53B ILE* 2.9 39.9 + - + -
54B PRO* 3.7 10.3 - - + +
56B SER* 1.3 73.8 - - - +
58B THR* 1.3 54.1 + - - +
60B LEU* 3.1 3.7 + - + +
61B ALA* 2.7 35.9 + - - +
68B PHE* 3.5 8.6 - + - -
70B LEU* 3.5 31.0 - - + -
77B MET* 4.6 13.0 - - - -
79B VAL* 3.9 29.2 - - + -
81B HIS* 4.3 10.3 - - + -
366B SER* 4.1 11.4 - - - -
390B VAL* 4.0 22.7 - - + -
392B THR* 3.8 16.6 - - - +
394B ASP* 6.2 0.2 - - - +
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Residues in contact with THR 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B PRO 3.1 15.1 + - - -
55B LYS* 3.9 7.1 - - - +
57B PHE* 1.3 77.8 - - - +
59B ARG* 1.3 63.8 + - - +
61B ALA* 3.2 10.4 + - - +
62B GLN* 3.2 33.3 + - - +
81B HIS* 2.9 33.6 + - + -
394B ASP* 4.5 7.8 + - - -
395B SER* 5.3 0.3 - - - -
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Residues in contact with ARG 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B GLN* 2.9 47.7 + - - +
55B LYS* 3.2 19.6 + - + +
56B SER* 3.1 9.4 + - - +
58B THR* 1.3 77.8 - - - +
60B LEU* 1.3 76.5 + - - +
62B GLN* 3.1 23.2 + - + +
63B ARG* 2.8 46.8 + - - +
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Residues in contact with LEU 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B PRO* 4.0 9.0 - - + -
47B GLN* 3.8 29.8 - - + +
48B LEU* 4.3 16.8 - - + -
56B SER 2.8 25.5 + - - +
57B PHE* 3.5 2.2 - - - +
59B ARG* 1.3 85.3 - - - +
61B ALA* 1.3 57.0 + - - +
63B ARG* 3.3 1.9 + - + +
64B PHE* 3.0 57.8 + - + +
68B PHE* 3.4 34.7 - - + -
70B LEU* 4.0 15.7 - - + -
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Residues in contact with ALA 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B PHE 2.7 18.6 + - - +
58B THR 3.2 6.6 + - - +
60B LEU* 1.3 72.3 - - - +
62B GLN* 1.3 67.5 + - - +
65B GLY* 3.1 37.8 + - - +
66B PRO* 5.0 0.4 - - + -
68B PHE* 3.6 2.9 - - + -
81B HIS* 3.5 37.7 - - + +
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Residues in contact with GLN 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B THR* 3.2 31.4 + - - +
59B ARG* 3.1 14.5 + - + +
61B ALA* 1.3 81.6 - - - +
63B ARG* 1.3 61.6 + - + +
65B GLY 4.7 1.0 + - - -
81B HIS* 6.1 0.8 - - - -
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Residues in contact with ARG 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B PRO* 4.1 7.5 - - - +
37B PHE 5.6 0.4 - - - +
47B GLN* 3.2 19.0 + - - -
59B ARG* 2.8 43.3 + - - +
60B LEU* 3.3 4.9 + - - +
62B GLN* 1.3 80.1 - - - +
64B PHE* 1.3 102.1 + - + +
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Residues in contact with PHE 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B PRO* 3.9 25.8 - - + +
35B GLY* 3.5 30.3 - - - -
36B PRO* 3.4 30.7 - - + -
60B LEU* 3.0 35.6 + - + +
63B ARG* 1.3 124.6 - - + +
65B GLY* 1.3 62.9 + - - +
66B PRO* 4.6 0.2 - - - +
67B VAL 3.9 4.9 - - - +
68B PHE* 4.0 17.9 - - + -
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Residues in contact with GLY 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B ALA* 3.1 33.6 + - - -
62B GLN 4.6 1.4 + - - -
63B ARG 3.9 0.6 - - - -
64B PHE* 1.3 81.6 - - - +
66B PRO* 1.3 70.5 - - - +
67B VAL 3.5 0.9 - - - -
68B PHE* 3.5 12.6 - - - -
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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