Contacts of the strand formed by residues 62 - 68 (chain B) in PDB entry 3U8Z
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 62 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47B PHE* 3.5 15.1 - - + -
56B LEU* 3.7 17.9 - - + -
58B GLU 3.5 26.0 - - - -
59B THR 2.9 10.7 + - - +
60B TRP 4.3 3.8 - - - +
61B PHE* 1.3 87.6 - - + +
63B GLY* 1.3 58.6 + - - +
96B PHE* 3.6 33.9 - + + -
97B LEU* 3.4 4.9 - - - +
98B ALA* 3.7 29.2 - - + -
99B LYS* 4.7 6.0 - - - +
100B PHE* 5.7 0.9 - - - -
114B THR* 3.7 16.4 - - - -
117B LEU* 4.0 33.4 - - + -
118B PHE* 3.7 20.9 - + - -
121B GLN* 5.3 0.7 - - - -
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Residues in contact with GLY 63 (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 PHE* 3.8 11.0 - - - -
62B PHE* 1.3 75.0 - - - +
64B LEU* 1.3 63.6 + - - -
74B TRP* 3.5 18.8 - - - -
77B MET* 5.7 3.6 - - - -
95B HIS 3.6 0.3 - - - +
96B PHE* 3.6 8.0 - - - -
97B LEU 3.0 29.4 + - - +
99B LYS* 5.2 2.2 - - - -
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Residues in contact with LEU 64 (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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26B ILE* 3.8 29.8 - - + -
46B LEU* 4.0 19.5 - - + +
47B PHE* 4.0 34.0 - - + +
50B VAL* 4.6 3.4 - - + -
63B GLY* 1.3 71.3 - - - -
65B GLN* 1.3 58.9 + - - +
66B TYR* 4.2 0.7 - - - -
74B TRP* 3.6 3.8 - - - +
75B LEU* 2.8 63.9 + - + +
77B MET* 5.1 4.1 - - + +
94B PHE* 3.8 14.1 - - + -
95B HIS 3.6 1.1 - - - -
96B PHE* 3.9 28.0 - - + -
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Residues in contact with GLN 65 (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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64B LEU* 1.3 72.8 - - - +
66B TYR* 1.3 63.8 + - - +
67B THR* 5.0 7.1 - - - +
72B VAL* 3.5 37.4 - - + +
73B ALA 3.3 16.4 - - - +
74B TRP* 3.6 28.3 - - + -
94B PHE* 3.4 7.9 - - - -
95B HIS* 2.8 53.7 + - + +
97B LEU* 3.7 23.7 - - + +
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Residues in contact with TYR 66 (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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65B GLN* 1.3 79.6 - - - +
67B THR* 1.4 70.6 + - - +
68B ILE* 3.7 34.3 - - + +
73B ALA* 2.8 42.2 + - + +
74B TRP 3.7 9.0 + - - -
75B LEU* 3.5 35.8 - - + +
76B LYS 5.4 0.3 + - - -
93B THR 4.3 9.4 - - - +
94B PHE* 3.8 28.9 - + + -
95B HIS* 5.6 2.2 - - - -
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Residues in contact with THR 67 (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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70A ASP* 5.9 2.2 - - - +
65B GLN* 5.0 6.7 - - - +
66B TYR* 1.4 85.0 - - - +
68B ILE* 1.3 63.7 + - - +
69B LYS 4.0 6.3 + - - +
70B ASP* 5.1 6.3 - - - +
71B THR 3.3 19.1 - - - +
72B VAL* 4.5 9.6 - - + -
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Residues in contact with ILE 68 (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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66B TYR* 3.7 35.4 + - + +
67B THR* 1.3 70.3 - - - +
69B LYS* 1.4 66.1 + - + +
70B ASP 2.8 15.9 + - - -
71B THR* 2.9 27.9 + - - +
73B ALA* 3.8 13.9 - - + +
291B ARG* 4.4 14.8 + - + -
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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