Contacts of the helix formed by residues 45 - 50 (chain I) in PDB entry 4XLN
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 GLN 45 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31I GLN* 3.3 18.6 - - - +
36I PRO 4.9 2.9 - - - +
39I ARG* 3.2 36.4 + - + +
41I ASN* 3.5 31.2 - - + +
42I VAL 3.9 0.6 + - - -
43I GLY 3.2 1.2 - - - -
44I ILE* 1.3 78.1 - - - +
46I ALA* 1.3 57.3 + - - +
48I PHE* 3.7 3.4 - - - -
49I LYS* 2.5 41.7 + - + +
68I PHE* 3.9 22.5 - - + -
69I LEU 5.3 0.5 - - - +
70I GLU* 4.9 1.0 - - - -
71I TYR* 3.1 33.9 + - - -
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Residues in contact with ALA 46 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41I ASN 3.1 19.9 + - - +
42I VAL* 3.7 6.3 - - + -
43I GLY 2.8 22.2 + - - +
45I GLN* 1.3 76.9 - - - +
47I ALA* 1.3 62.0 + - - +
48I PHE 3.0 0.7 + - - -
49I LYS* 4.1 6.1 - - - +
50I GLU* 3.1 47.2 + - - +
288I ARG* 6.0 3.4 - - - +
341I ALA* 5.9 0.4 - - + -
345I ARG* 4.0 9.2 - - - +
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Residues in contact with ALA 47 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43I GLY 3.0 12.8 + - - +
44I ILE* 3.9 5.6 - - - +
46I ALA* 1.3 75.9 - - - +
48I PHE* 1.3 50.8 + - - +
50I GLU* 4.5 1.3 - - - -
51I THR* 2.7 33.1 + - - +
341I ALA* 3.7 11.0 - - + +
344I PHE* 4.0 13.9 - - + -
345I ARG* 3.6 42.2 - - + +
348I LEU* 3.3 10.4 - - - +
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Residues in contact with PHE 48 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44I ILE* 3.2 37.6 + - + +
45I GLN* 3.0 10.9 + - - +
46I ALA 3.0 0.6 - - - -
47I ALA* 1.3 76.0 - - - +
49I LYS* 1.3 66.1 + - - +
50I GLU 3.1 1.3 - - - -
51I THR* 2.7 18.8 + - - -
52I PHE* 3.3 20.9 + + - -
68I PHE* 3.5 36.6 - + + -
71I TYR* 3.7 41.5 - + + -
94I LEU* 4.4 1.8 - - + -
96I ALA* 4.6 6.1 - - + -
115I LEU* 3.8 27.6 - - + -
344I PHE* 4.0 8.7 - + - -
348I LEU* 3.5 23.3 - - + -
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Residues in contact with LYS 49 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41I ASN* 3.1 34.5 - - + +
45I GLN* 2.5 25.9 + - + +
46I ALA* 3.9 7.0 - - - +
48I PHE* 1.3 73.2 - - - +
50I GLU* 1.3 75.9 + - - +
51I THR 3.3 0.2 - - - -
52I PHE* 2.8 28.6 + - - +
68I PHE* 4.8 11.2 - - + -
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Residues in contact with GLU 50 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46I ALA* 3.1 25.4 + - - +
47I ALA* 5.0 2.0 - - - +
48I PHE 3.1 0.8 - - - -
49I LYS* 1.3 90.5 - - - +
51I THR* 1.3 59.1 + - + +
52I PHE 3.1 11.2 + - - +
168I ARG* 4.9 1.2 + - - -
264I PRO* 4.1 9.3 - - + +
265I LYS* 3.1 51.0 + - + +
268I ASP* 3.5 15.9 - - - +
288I ARG* 4.7 6.1 + - - -
345I ARG* 3.0 40.6 + - + -
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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