Contacts of the helix formed by residues 50 - 61 (chain B) in PDB entry 1XVI
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 THR 50 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49B LYS* 1.3 74.8 - - - +
51B SER* 1.3 63.4 + - - +
52B ALA 3.6 1.4 + - - -
53B GLU* 3.2 14.5 + - - +
54B MET* 2.8 27.3 + - - +
71B GLU* 3.7 9.6 - - - -
139B LEU 2.7 22.1 + - - +
140B THR* 3.5 27.4 - - - +
142B LEU 3.7 16.2 - - - -
143B HIS* 3.7 32.3 - - + +
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Residues in contact with SER 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B THR* 1.3 73.7 - - - +
52B ALA* 1.3 58.1 + - - +
54B MET* 3.4 1.8 + - - +
55B LEU* 2.9 41.3 + - - +
68B LEU* 5.3 2.5 - - - -
70B ALA* 3.7 13.1 - - - +
71B GLU* 3.7 7.1 + - - -
75B VAL* 3.8 20.4 - - - -
77B GLN* 4.6 0.8 + - - -
90B ARG* 3.2 27.0 + - - -
142B LEU 5.7 1.1 - - - -
144B GLU* 3.4 21.6 + - - -
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Residues in contact with ALA 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B THR* 3.2 1.8 + - - +
51B SER* 1.3 77.2 + - - +
53B GLU* 1.3 64.3 + - - +
55B LEU* 3.5 9.1 + - - +
56B TYR* 3.2 22.5 + - - +
139B LEU* 4.1 23.6 - - + +
142B LEU* 4.0 33.3 + - + +
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Residues in contact with GLU 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 48.4 - - + +
50B THR* 3.2 19.9 + - - +
52B ALA* 1.3 75.8 - - - +
54B MET* 1.3 60.0 + - - +
56B TYR* 3.2 4.2 + - + +
57B LEU* 2.9 38.4 + - + +
132B LEU* 4.0 13.0 - - - +
136B GLN* 4.2 14.3 + - - +
139B LEU* 3.9 18.9 - - + +
140B THR* 2.8 38.4 + - - +
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Residues in contact with MET 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B LEU* 4.5 18.3 - - + +
46B CYS 4.9 0.9 - - - -
47B SER* 3.1 36.1 - - - -
49B LYS* 3.6 32.5 - - + +
50B THR 2.8 27.8 + - - +
51B SER 3.6 5.2 - - - +
53B GLU* 1.3 75.0 - - - +
55B LEU* 1.3 53.3 + - - +
57B LEU* 3.6 13.4 - - + +
58B GLN* 2.7 35.7 + - - +
68B LEU* 3.8 21.6 - - + +
69B ILE 4.0 11.9 - - - +
70B ALA* 3.7 7.0 - - + -
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Residues in contact with LEU 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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51B SER* 2.9 39.4 + - - +
52B ALA* 3.8 8.3 - - - +
54B MET* 1.3 73.8 - - - +
56B TYR* 1.3 64.9 + - - +
58B GLN* 3.6 19.5 + - - +
59B LYS* 3.1 25.6 + - - +
64B GLN* 5.3 6.3 - - + +
68B LEU* 4.1 6.5 - - + -
77B GLN* 3.6 41.7 - - + +
90B ARG* 3.7 10.5 - - - +
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Residues in contact with TYR 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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24B TYR 3.8 5.7 + - - -
25B ASP* 2.5 40.9 + - - -
52B ALA 3.2 13.4 + - - +
53B GLU* 3.7 6.1 - - - +
55B LEU* 1.3 74.9 - - - +
57B LEU* 1.3 83.2 + - + +
59B LYS* 3.2 20.9 + - - +
60B THR* 3.1 39.5 + - + +
136B GLN* 3.9 28.7 + - + +
139B LEU* 3.9 21.3 - - + -
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Residues in contact with LEU 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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19B LEU* 4.1 26.2 - - + -
24B TYR 5.8 0.4 - - - +
27B GLN* 4.9 8.3 - - - +
45B LEU* 5.2 2.0 - - + -
49B LYS* 3.8 36.1 - - + -
53B GLU* 2.9 24.8 + - + +
54B MET* 3.8 14.1 - - + +
56B TYR* 1.3 95.9 - - + +
58B GLN* 1.3 60.7 + - - +
60B THR* 3.1 12.3 + - - +
61B LEU* 3.1 35.4 + - + +
136B GLN* 4.0 17.3 - - - +
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Residues in contact with GLN 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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43B VAL 5.4 0.4 + - - -
45B LEU* 3.8 17.5 - - + +
54B MET 2.7 22.1 + - - +
55B LEU* 3.6 17.6 - - - +
56B TYR 3.3 0.2 - - - -
57B LEU* 1.3 71.7 - - - +
59B LYS* 1.3 61.9 + - - +
61B LEU* 3.2 3.1 + - - -
62B GLY 3.2 4.5 + - - -
63B LEU* 2.9 62.6 + - + +
64B GLN* 3.6 13.0 - - - +
65B GLY 3.9 4.5 + - - -
66B LEU* 3.0 28.5 + - - +
67B PRO 3.5 9.9 + - - -
68B LEU* 3.5 26.6 - - + +
77B GLN* 5.1 0.5 - - - +
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Residues in contact with LYS 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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55B LEU 3.1 16.2 + - - +
56B TYR* 3.2 22.2 + - - +
58B GLN* 1.3 76.7 - - - +
60B THR* 1.3 61.5 + - + +
62B GLY* 3.2 13.0 + - - -
64B GLN* 3.8 46.4 - - + +
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Residues in contact with THR 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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24B TYR 4.9 0.6 + - - +
25B ASP* 3.6 32.9 - - + +
27B GLN* 3.4 26.5 + - - +
30B ALA* 3.2 18.6 - - - +
56B TYR* 3.1 42.3 + - + +
57B LEU* 3.1 19.1 + - - +
59B LYS* 1.3 78.1 - - + +
61B LEU* 1.3 56.7 + - - +
62B GLY 3.3 1.6 - - - -
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Residues in contact with LEU 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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18B LEU* 4.4 8.7 - - + +
19B LEU* 3.8 27.6 - - + -
27B GLN* 3.8 27.4 - - + +
29B ALA* 3.8 25.1 - - + -
30B ALA* 3.5 14.8 - - - +
33B LEU* 3.4 32.5 - - + +
45B LEU* 4.0 30.1 - - + -
57B LEU* 3.1 21.8 + - + +
58B GLN 3.2 3.6 + - - +
59B LYS 3.2 0.2 - - - -
60B THR* 1.3 78.4 - - - +
62B GLY* 1.3 62.0 + - - +
63B LEU* 3.4 6.0 - - + +
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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