Contacts of the strand formed by residues 42 - 49 (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 LEU 42 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A LEU* 4.2 24.9 - - + -
36A ILE* 4.3 14.1 - - + -
38A SER 5.0 1.6 - - - +
39A TYR* 3.0 28.5 + - + +
40A GLU* 4.3 3.9 - - - +
41A GLU* 1.3 79.6 - - - +
43A ALA* 1.3 64.6 + - - +
44A ALA 4.5 2.9 - - - +
45A VAL* 4.2 13.5 - - + -
67A MET* 4.1 25.6 - - + -
70A VAL* 4.1 24.0 - - + +
71A PRO* 4.7 2.8 - - - +
92A ALA* 4.3 19.1 - - + -
93A LEU 3.6 10.3 - - - +
94A TRP* 4.6 4.9 - - + -
95A ASN* 4.4 1.6 - - - -
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Residues in contact with ALA 43 (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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2A VAL* 5.3 5.4 - - + -
41A GLU 3.6 3.8 + - - -
42A LEU* 1.3 72.9 - - - +
44A ALA* 1.3 61.0 + - + +
71A PRO* 3.2 20.5 - - - +
93A LEU* 2.8 29.9 + - + +
95A ASN* 3.8 23.4 - - - +
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Residues in contact with ALA 44 (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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42A LEU* 3.3 2.1 - - - +
43A ALA* 1.3 81.9 - - + +
45A VAL* 1.3 71.4 + - - +
46A ILE* 5.3 5.6 - - + -
70A VAL* 4.4 1.8 - - - -
71A PRO* 3.2 23.6 - - + +
92A ALA* 4.5 0.2 - - - +
93A LEU* 2.9 43.2 + - + +
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Residues in contact with VAL 45 (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* 4.3 7.0 - - + -
42A LEU* 4.2 17.3 - - + -
44A ALA* 1.3 80.5 - - - +
46A ILE* 1.3 65.8 + - - +
47A PHE* 3.7 19.5 - - + -
67A MET* 4.8 5.6 - - - -
70A VAL* 3.9 17.7 - - + -
71A PRO 2.9 7.1 + - - +
72A LEU* 3.2 18.0 - - + +
73A LEU 3.1 22.7 + - - +
90A VAL* 3.5 30.5 - - + -
91A LEU 3.5 4.5 - - - +
92A ALA* 4.2 11.0 - - + -
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Residues in contact with ILE 46 (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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44A ALA* 5.3 6.3 - - + -
45A VAL* 1.3 79.5 - - - +
47A PHE* 1.3 70.2 + - - +
48A THR* 5.3 4.7 - - + -
73A LEU* 3.3 30.7 - - + +
74A SER* 5.2 0.9 - - - -
75A ALA* 5.6 3.8 - - + +
90A VAL* 3.5 3.5 - - - +
91A LEU* 2.8 61.9 + - + +
93A LEU* 4.7 15.7 - - + -
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Residues in contact with PHE 47 (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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23A THR* 3.9 18.8 - - + -
27A LEU* 4.1 9.2 - - + -
45A VAL* 3.7 27.4 - - + -
46A ILE* 1.3 77.8 - - - +
48A THR* 1.3 66.8 + - - +
58A PRO* 3.6 31.2 - - + -
59A ALA* 4.3 12.6 - - - -
62A ALA* 4.1 21.1 - - + -
67A MET* 5.8 0.2 - - - -
72A LEU* 4.1 17.3 - - + -
73A LEU 2.8 20.6 + - - +
74A SER* 3.2 9.0 - - - -
75A ALA* 2.9 24.5 + - - +
88A ILE* 4.7 2.2 - - + -
89A ARG 3.2 7.4 - - - +
90A VAL* 3.8 28.0 - - + -
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Residues in contact with THR 48 (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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46A ILE* 5.3 5.8 - - + -
47A PHE* 1.3 79.7 - - - +
49A VAL* 1.3 67.9 + - - +
74A SER* 6.1 0.2 - - - -
75A ALA* 3.1 22.2 - - + +
76A ARG 4.8 4.3 - - - +
77A GLU* 4.0 21.2 + - - +
87A VAL 3.8 0.5 - - - +
88A ILE* 3.5 1.7 - - - +
89A ARG* 2.9 58.7 + - + +
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Residues in contact with VAL 49 (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* 5.5 2.7 - - + -
48A THR* 1.3 79.9 - - - +
50A THR* 1.3 64.7 + - - +
53A LEU* 3.6 30.7 - - + +
56A ALA 5.4 2.0 - - - +
58A PRO* 3.8 30.3 - - + -
74A SER* 6.3 1.8 - - - -
75A ALA 3.1 10.7 + - - +
76A ARG* 3.4 13.4 - - + +
77A GLU* 2.9 23.0 + - - -
87A VAL 3.5 4.5 - - - +
88A ILE* 4.1 18.8 - - + -
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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