Contacts of the helix formed by residues 48 - 60 (chain B) in PDB entry 3UYS
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 48 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40B GLU* 2.6 12.6 + - - +
47B PRO* 1.3 76.1 - - - +
49B LEU* 1.3 69.0 + - - +
50B HIS* 2.8 4.5 + - - -
51B ILE* 3.0 18.1 + - + +
52B GLU* 3.4 16.6 + - + +
151B GLY* 4.5 26.1 + - - +
152B LEU* 6.2 0.2 - - - +
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Residues in contact with LEU 49 (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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38B LYS* 3.7 39.0 - - + +
40B GLU* 2.8 33.9 + - + +
48B GLN* 1.3 75.0 - - - +
50B HIS* 1.3 69.1 + - - +
52B GLU* 3.3 8.3 + - - +
53B SER* 2.9 20.9 + - - -
78B ASN* 2.9 47.8 - - + +
79B VAL* 3.6 11.0 - - - +
80B MET* 4.0 21.8 - - + -
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Residues in contact with HIS 50 (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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40B GLU* 5.0 0.8 + - - -
47B PRO 5.6 1.1 - - - +
48B GLN 2.8 4.0 + - - -
49B LEU* 1.3 78.7 - - - +
51B ILE* 1.3 75.1 + - + +
53B SER* 2.9 23.2 + - - -
54B LYS* 2.9 37.3 + - + +
71B CYS* 6.0 3.9 - - + +
78B ASN* 5.6 4.9 + - - +
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Residues in contact with ILE 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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47B PRO 4.8 11.7 - - - +
48B GLN* 3.0 14.2 + - + +
50B HIS* 1.3 82.0 - - + +
52B GLU* 1.3 69.4 + - - +
54B LYS* 2.6 21.5 + - + +
55B ILE* 3.1 21.0 + - + +
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Residues in contact with GLU 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LYS* 2.9 31.6 + - - +
48B GLN* 3.4 13.2 + - + +
49B LEU* 3.3 13.4 + - - +
51B ILE* 1.3 77.2 - - - +
53B SER* 1.3 55.9 + - - +
55B ILE* 2.4 42.1 + - - +
56B TYR* 3.0 44.7 + - + -
80B MET* 4.6 4.9 - - + +
149B ASP* 3.7 8.4 - - - +
150B PHE* 3.3 32.5 + - + +
151B GLY* 4.6 6.2 + - - +
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Residues in contact with SER 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 LEU* 2.9 14.1 + - - -
50B HIS* 2.9 22.4 + - - -
52B GLU* 1.3 76.9 - - - +
54B LYS* 1.3 61.3 + - - +
55B ILE 3.2 0.2 + - - -
56B TYR* 3.2 5.8 + - - +
57B LYS* 2.9 35.5 + - - +
68B ILE* 5.0 0.9 - - - +
71B CYS* 3.4 23.6 - - - -
80B MET* 3.7 28.9 - - - -
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Residues in contact with LYS 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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50B HIS* 2.9 40.1 + - + +
51B ILE* 2.6 19.0 + - + +
53B SER* 1.3 74.8 + - - +
55B ILE* 1.3 57.4 + - + -
57B LYS* 3.6 23.5 - - + +
58B MET* 2.9 41.4 + - + +
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Residues in contact with ILE 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 ILE* 3.7 18.2 - - + +
52B GLU* 2.4 32.9 + - - +
54B LYS* 1.3 67.2 - - - +
56B TYR* 1.3 63.0 + - - +
58B MET* 2.8 14.3 + - + +
59B MET* 2.8 27.5 + - + +
124B PHE* 3.7 37.2 - - + -
150B PHE* 3.4 56.3 - - + +
153B ALA* 3.9 11.0 - - + +
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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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52B GLU* 3.0 47.3 + - + -
53B SER 3.5 4.0 - - - +
55B ILE* 1.3 76.3 - - - +
57B LYS* 1.3 51.3 + - - +
59B MET* 2.5 27.5 + - - +
60B GLN* 2.6 22.8 + - - +
65B ILE* 4.4 6.1 - - + -
66B PRO* 3.1 38.0 - - + +
68B ILE* 3.0 32.3 - - + -
80B MET* 3.8 7.9 - - + -
82B MET* 3.5 22.9 - - + +
147B ILE 4.8 0.4 - - - -
148B ILE* 4.0 7.6 - - - +
149B ASP 3.3 21.3 + - - -
150B PHE* 4.0 21.8 - + - -
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Residues in contact with LYS 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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53B SER* 2.9 30.0 + - - +
54B LYS* 3.6 30.1 - - + +
56B TYR* 1.3 75.9 - - + +
58B MET* 1.3 62.8 + - + +
60B GLN* 3.1 28.9 + - + +
68B ILE* 4.3 18.9 + - + +
69B ARG 6.3 0.2 - - - -
70B TRP* 5.9 1.6 - - - +
71B CYS* 4.1 29.5 - - - +
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Residues in contact with MET 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 LYS* 2.9 35.6 + - + +
55B ILE* 2.8 13.6 + - + +
57B LYS* 1.3 77.4 - - + +
59B MET* 1.3 62.9 + - - +
60B GLN 3.3 2.0 + - - +
122B LYS* 4.0 23.0 + - + +
124B PHE* 3.7 39.9 - - + -
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Residues in contact with MET 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 ILE* 2.8 21.6 + - + +
56B TYR* 2.5 21.4 + - - +
58B MET* 1.3 73.3 - - + +
60B GLN* 1.3 61.2 + - - -
62B GLY 3.5 2.6 + - - -
65B ILE* 3.6 27.4 - - + +
118B TYR* 2.8 29.3 + - + -
119B ILE* 3.6 27.1 - - + +
122B LYS* 3.4 25.6 - - + -
124B PHE* 3.5 45.8 - - + -
150B PHE* 4.0 20.4 - - + -
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Residues in contact with GLN 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B TYR* 2.6 38.2 + - - +
57B LYS* 3.1 20.2 + - + +
58B MET 3.3 2.7 + - - +
59B MET* 1.3 79.2 - - - +
61B GLY* 1.3 61.0 + - - +
65B ILE* 4.5 2.5 - - - +
66B PRO 4.0 10.0 + - - -
67B THR* 3.3 17.7 - - + +
68B ILE* 2.8 33.3 + - - +
118B TYR* 3.0 13.5 + - - -
122B LYS* 5.1 3.5 + - - -
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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