Contacts of the helix formed by residues 57 - 65 (chain A) in PDB entry 1UFY
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 PHE 57 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A ILE* 5.1 0.2 - - - -
20A HIS* 3.9 7.4 + - - -
56A ALA* 1.3 75.5 - - - +
58A PRO* 1.3 71.3 - - + +
59A ALA* 4.1 6.5 - - + +
60A GLU* 3.0 41.6 + - + +
61A ALA 3.7 2.9 + - - -
63A ARG* 5.8 0.2 - - - +
74A SER* 4.3 16.4 - - - +
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Residues in contact with PRO 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ILE* 4.9 6.5 - - + -
23A THR* 3.7 22.6 - - - +
47A PHE* 3.6 37.9 - - + -
49A VAL* 3.8 29.8 - - + -
56A ALA 3.6 8.7 - - - +
57A PHE* 1.3 82.3 - - + +
59A ALA* 1.3 62.7 + - - +
61A ALA* 3.0 16.4 + - + +
62A ALA* 3.1 10.7 + - - +
74A SER* 4.5 13.7 - - - +
88A ILE* 4.5 5.4 - - + -
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Residues in contact with ALA 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A PHE* 4.3 9.1 - - + -
57A PHE* 3.1 7.5 - - + +
58A PRO* 1.3 79.2 - - - +
60A GLU* 1.3 61.9 + - - +
62A ALA* 3.2 4.4 + - - +
63A ARG* 3.0 42.9 + - - +
72A LEU* 3.8 32.9 - - + +
73A LEU* 5.5 0.9 - - - +
74A SER* 5.4 7.1 + - - +
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Residues in contact with GLU 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A HIS* 4.1 13.5 - - + +
57A PHE* 3.0 33.8 + - + +
59A ALA* 1.3 77.4 - - - +
61A ALA* 1.3 60.8 + - - +
63A ARG* 2.9 35.4 + - - +
64A GLN* 3.1 27.0 + - - +
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Residues in contact with ALA 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A HIS* 3.6 42.4 - - + +
23A THR* 3.7 17.5 - - + +
24A ARG* 3.7 10.4 - - + +
27A LEU* 5.1 0.2 - - - -
57A PHE 3.7 2.0 + - - -
58A PRO 3.0 10.8 + - - +
60A GLU* 1.3 75.1 - - - +
62A ALA* 1.3 66.3 + - - +
64A GLN* 3.0 29.7 + - - +
65A ILE* 3.4 4.9 + - - +
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Residues in contact with ALA 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LEU* 3.7 29.3 - - + +
47A PHE* 4.1 6.7 - - + -
58A PRO 3.1 10.9 + - - +
59A ALA 3.2 8.7 + - - +
61A ALA* 1.3 75.7 - - - +
63A ARG* 1.3 60.3 + - - +
65A ILE* 3.2 15.2 + - - +
66A GLY 3.3 0.5 + - - -
67A MET* 3.0 30.8 + - + +
72A LEU* 3.6 20.9 - - + -
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Residues in contact with ARG 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A PHE* 5.8 0.2 - - - +
59A ALA* 3.0 29.8 + - - +
60A GLU* 2.9 43.3 + - - +
61A ALA 3.2 0.4 - - - -
62A ALA* 1.3 74.3 - - - +
64A GLN* 1.3 58.4 + - - +
66A GLY* 3.0 13.2 + - - -
67A MET 3.9 8.2 + - - +
68A HIS* 3.4 61.4 + - + +
72A LEU* 3.7 23.3 - - + +
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Residues in contact with GLN 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A HIS* 3.5 18.6 + - - +
24A ARG* 2.8 37.3 + - - -
60A GLU* 3.1 10.8 + - - +
61A ALA* 3.0 25.0 + - - +
63A ARG* 1.3 77.4 - - - +
65A ILE* 1.3 59.6 + - - +
66A GLY 3.4 0.8 + - - -
301A MES 5.4 3.1 - - - +
304A MES 3.4 40.2 + - - +
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Residues in contact with ILE 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ARG* 4.0 29.6 - - + +
27A LEU* 4.0 28.3 - - + -
28A LEU* 3.9 26.2 - - + -
39A TYR* 2.7 43.4 + - - +
61A ALA 3.9 5.4 - - - +
62A ALA* 3.3 13.2 - - - +
63A ARG 3.2 0.2 - - - -
64A GLN* 1.3 79.2 - - - +
66A GLY* 1.3 56.3 + - - +
67A MET* 4.2 8.7 - - + -
301A MES 3.9 28.7 - - - +
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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