Contacts of the strand formed by residues 69 - 75 (chain D) in PDB entry 3U1K
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 GLY 69 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67D ALA* 2.9 8.5 + - - +
68D ASP* 1.3 78.7 - - - +
70D SER* 1.3 63.8 + - - -
83D THR* 3.2 4.2 - - - -
84D ALA* 2.9 33.7 + - - -
176D ALA* 3.6 22.9 - - - -
179D LEU* 5.2 1.1 - - - -
180D SER* 3.6 6.0 - - - -
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Residues in contact with SER 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D SER* 2.6 31.5 + - - -
61D GLY 6.0 0.2 - - - -
63D LEU 3.0 21.2 + - - -
64D ALA* 3.6 28.0 + - - +
65D ARG* 5.4 1.1 - - - -
67D ALA* 4.8 1.1 - - - -
69D GLY* 1.3 76.7 - - - -
71D ALA* 1.3 61.8 + - - +
81D MET* 4.2 6.9 - - - +
82D VAL 3.4 9.8 + - - -
83D THR* 4.1 4.7 - - - +
176D ALA* 4.1 4.8 + - - +
179D LEU* 4.1 7.4 - - - +
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Residues in contact with ALA 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D ILE* 5.2 0.2 - - + -
59D SER 3.4 9.0 - - - +
60D SER* 4.2 2.0 - - - +
70D SER* 1.3 77.9 + - - +
72D VAL* 1.3 65.0 + - - +
73D VAL* 5.2 1.6 - - + -
80D VAL 3.9 0.5 - - - +
81D MET* 3.3 6.5 - - - +
82D VAL* 2.9 32.2 + - - +
172D GLY* 4.1 7.1 - - - +
175D VAL* 3.3 39.5 - - + -
176D ALA 3.8 8.1 - - - +
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Residues in contact with VAL 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377C PHE* 5.7 2.5 - - + -
57D GLU 3.4 2.6 - - - +
58D ILE* 3.5 2.4 - - - +
59D SER* 2.9 59.6 + - - +
60D SER* 4.5 4.0 - - - +
62D LYS* 6.2 3.6 - - + -
63D LEU* 5.3 12.8 - - + +
71D ALA* 1.3 75.4 - - - +
73D VAL* 1.3 72.6 + - - +
74D GLN* 4.9 7.0 - - + +
79D ALA* 4.6 8.5 - - + -
80D VAL 3.3 9.4 - - - +
81D MET* 4.5 7.2 - - + -
157D LEU* 4.3 19.1 - - + -
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Residues in contact with VAL 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D LEU* 3.7 31.9 - - + -
57D GLU 3.3 5.4 - - - +
58D ILE* 4.6 8.7 - - + -
71D ALA* 5.2 0.2 - - + -
72D VAL* 1.3 80.3 - - - +
74D GLN* 1.3 63.8 + - - +
79D ALA* 3.5 0.3 - - - -
80D VAL* 2.8 35.8 + - - +
168D LEU* 3.8 26.2 - - + +
171D ASN* 4.1 9.9 - - + +
172D GLY* 3.6 33.4 - - - +
175D VAL* 4.5 12.1 - - + -
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Residues in contact with GLN 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377C PHE* 4.5 12.2 - - - -
56D LEU* 3.6 1.2 - - - -
57D GLU* 2.7 60.8 + - + +
72D VAL* 5.0 6.7 - - + +
73D VAL* 1.3 76.8 - - - +
75D SER* 1.3 64.2 + - - +
76D GLY 2.9 23.1 + - - +
77D ASP* 4.0 14.5 + - - +
78D THR 3.2 16.2 - - - +
79D ALA* 4.0 18.2 - - + +
168D LEU* 4.2 3.1 - - - -
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Residues in contact with SER 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D LEU* 5.6 1.4 - - - +
54D ARG* 4.9 6.0 - - - +
55D LYS 2.9 22.0 + - - -
56D LEU* 3.1 22.5 - - - +
57D GLU* 5.0 0.4 - - - -
74D GLN* 1.3 69.2 - - - +
76D GLY* 1.3 67.6 + - - +
77D ASP 3.2 0.2 + - - -
78D THR* 3.0 19.2 + - - +
163D ASN* 3.5 29.5 - - - +
168D LEU* 3.7 16.2 - - - +
203D ASN* 5.8 1.0 + - - -
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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