Contacts of the strand formed by residues 60 - 65 (chain I) in PDB entry 4EUP
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 60 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36I ARG* 4.1 22.9 - - - -
46I ILE* 4.1 38.6 - - + -
47I MET* 3.6 22.8 - - + +
55I LYS 4.3 0.3 - - - +
56I GLU* 3.7 0.2 - - - -
57I ASP* 3.0 45.7 + - + +
59I ARG* 1.3 84.6 - - + +
61I THR* 1.3 59.9 + - - +
73I LEU* 4.0 11.2 - - + -
74I LEU 3.4 7.2 - - - -
75I ILE* 3.8 36.3 - - + -
76I ARG* 3.4 6.1 + - - -
82I ASP* 5.1 5.8 - - - -
86I TYR* 5.0 3.1 - + - -
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Residues in contact with THR 61 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54I ASP* 4.1 18.6 - - + +
55I LYS 3.8 3.8 - - - +
56I GLU* 3.7 22.2 + - + +
59I ARG 3.6 1.2 + - - -
60I PHE* 1.3 69.8 + - - +
62I ALA* 1.3 71.2 + - - +
63I GLN* 5.7 0.7 - - + -
73I LEU* 3.4 4.0 - - - -
74I LEU* 2.7 59.8 + - + +
76I ARG* 2.9 35.2 + - - -
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Residues in contact with ALA 62 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34I TRP* 4.5 3.8 - - + +
47I MET* 3.6 36.2 - - + -
49I ILE* 3.8 19.0 - - + +
54I ASP* 3.4 3.5 - - - -
55I LYS 3.1 31.3 + - - +
60I PHE 4.3 0.2 - - - -
61I THR* 1.3 79.0 - - - +
63I GLN* 1.3 61.1 + - - +
72I SER 3.4 12.6 - - - +
73I LEU* 4.3 3.1 - - + +
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Residues in contact with GLN 63 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49I ILE* 4.2 3.1 - - - -
53I GLY* 3.1 21.5 + - - +
54I ASP* 3.6 27.3 + - - +
61I THR* 5.7 1.3 - - + -
62I ALA* 1.3 73.4 - - - +
64I LEU* 1.3 66.3 + - - +
65I ASN* 5.8 5.8 - - - +
70I TYR 4.1 0.7 - - - +
71I VAL* 3.3 7.6 - - - +
72I SER* 2.9 43.8 + - - -
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Residues in contact with LEU 64 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24I TYR* 4.0 8.3 - - - +
32I PHE* 3.5 36.3 - - + -
49I ILE* 4.2 12.5 - - + +
50I TYR* 3.9 15.0 - - - +
51I SER 3.3 29.6 - - - +
52I ASN* 3.2 7.2 + - - +
53I GLY 3.0 27.6 + - - -
63I GLN* 1.3 81.9 + - - +
65I ASN* 1.3 66.1 + - - +
66I LYS* 3.8 22.7 - - + +
70I TYR 3.9 1.8 - - - +
71I VAL* 3.6 26.7 - - + -
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Residues in contact with ASN 65 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52I ASN* 3.4 5.0 + - - +
63I GLN* 5.8 6.2 - - - +
64I LEU* 1.3 74.2 - - - +
66I LYS* 1.3 58.3 + - - +
67I ALA* 3.5 13.2 + - - +
68I SER* 3.2 32.6 + - - -
69I GLN 2.8 23.4 + - - -
70I TYR* 2.9 26.3 + - + +
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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