Contacts of the helix formed by residues 50 - 59 (chain B) in PDB entry 1XK4
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 50 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B LEU* 4.9 0.2 - - - -
47B ARG 2.9 13.6 + - - -
48B LYS 3.2 1.9 - - - -
49B LYS* 1.3 80.0 - - - +
51B ALA* 1.3 60.3 + - - -
52B ASP 3.3 2.9 - - - -
53B VAL* 3.3 5.9 + - - -
54B TRP* 3.0 32.0 + - - -
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Residues in contact with ALA 51 (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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31B ARG 5.1 2.9 - - - +
34B LEU* 4.0 3.3 - - + +
35B LYS* 3.7 48.0 - - + +
38B LEU* 3.7 17.9 - - + +
47B ARG 4.8 0.8 + - - -
50B GLY* 1.3 71.0 - - - -
52B ASP* 1.3 61.7 + - - +
54B TRP* 3.3 2.1 + - - +
55B PHE* 2.8 30.2 + - - +
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Residues in contact with ASP 52 (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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31B ARG* 4.1 31.5 + - - +
50B GLY 3.3 0.8 - - - -
51B ALA* 1.3 80.7 - - - +
53B VAL* 1.3 61.6 + - + +
55B PHE* 3.3 5.7 + - - +
56B LYS* 3.0 24.6 + - - +
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Residues in contact with VAL 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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49B LYS* 3.2 50.9 - - + +
50B GLY* 3.3 3.4 + - - +
52B ASP* 1.3 78.6 - - + +
54B TRP* 1.3 61.1 + - - +
56B LYS* 3.4 6.3 + - - +
57B GLU* 3.1 24.1 + - - +
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Residues in contact with TRP 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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34B LEU* 4.1 7.0 - - + -
38B LEU* 3.9 26.9 - - + -
46B ILE* 2.9 55.2 + - + +
47B ARG 5.0 0.7 - - - -
49B LYS* 3.3 35.1 - - + +
50B GLY 3.0 22.5 + - - +
51B ALA 3.6 7.6 - - - +
53B VAL* 1.3 73.2 - - - +
55B PHE* 1.3 67.3 + - - +
57B GLU* 3.1 23.3 + - - +
58B LEU* 2.9 49.6 + - + +
74B LEU* 3.8 24.0 - - + -
77B LYS* 4.0 27.4 - - + -
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Residues in contact with PHE 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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29B VAL 3.7 3.4 - - - -
30B TYR 3.5 6.7 - - - -
31B ARG* 3.5 72.7 - - + +
34B LEU* 3.7 22.2 - - + +
51B ALA 2.8 21.1 + - - +
52B ASP* 3.7 8.3 - - - +
53B VAL 3.3 0.2 - - - -
54B TRP* 1.3 72.7 - - - +
56B LYS* 1.3 58.1 + - - +
58B LEU* 3.8 1.9 - - - +
59B ASP* 2.9 48.8 + - + +
64B GLY 3.4 34.1 - - - -
65B ALA* 3.7 8.5 - - - -
66B VAL* 3.6 16.2 - - + -
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Residues in contact with LYS 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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77A LYS* 5.9 2.6 - - - -
31B ARG* 5.2 8.0 - - - +
52B ASP 3.0 16.1 + - - +
53B VAL* 3.8 6.1 - - - +
54B TRP 3.2 0.2 - - - -
55B PHE* 1.3 80.4 - - - +
57B GLU* 1.3 62.2 + - - +
59B ASP* 3.9 14.1 + - - +
62B THR* 6.1 0.2 - - - +
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Residues in contact with GLU 57 (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 LYS* 2.8 32.6 + - - +
53B VAL* 3.1 14.7 + - + +
54B TRP* 3.4 19.1 - - + +
56B LYS* 1.3 79.1 - - - +
58B LEU* 1.3 62.3 + - + +
60B ILE* 3.6 17.7 - - - +
73B ILE* 4.9 5.5 - - + +
77B LYS* 2.6 42.3 + - - +
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Residues in contact with LEU 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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34B LEU* 4.1 28.7 - - + -
54B TRP* 2.9 35.1 + - + +
57B GLU* 1.3 75.6 - - + +
59B ASP* 1.3 61.6 + - - +
60B ILE* 2.9 14.6 + - - +
66B VAL* 3.8 22.9 - - + -
70B GLU* 3.2 43.1 - - - +
71B PHE* 5.0 1.1 - - - -
73B ILE* 3.6 25.1 - - + +
74B LEU* 3.6 31.2 - - + +
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Residues in contact with ASP 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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77A LYS* 4.7 2.3 - - - -
55B PHE* 2.9 29.9 + - + +
56B LYS* 3.9 10.5 + - - +
57B GLU 3.5 0.6 - - - -
58B LEU* 1.3 74.1 - - - +
60B ILE* 1.3 61.1 + - - +
61B ASN* 3.1 4.3 - - - +
62B THR* 3.1 25.6 + - + +
63B ASP* 3.0 5.5 - - - +
64B GLY* 2.9 27.9 + - - -
65B ALA 3.3 14.8 - - - +
66B VAL* 4.4 1.3 - - + +
70B GLU* 3.6 3.1 - - - -
2501B CA 2.2 29.4 - - - -
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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