Contacts of the strand formed by residues 78 - 86 (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 THR 78 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74D GLN* 3.2 5.7 - - - +
75D SER 3.0 33.7 + - - -
77D ASP* 1.3 77.8 - - - +
79D ALA* 1.3 60.4 + - - +
80D VAL* 4.5 2.2 - - + -
158D ALA 3.4 10.5 - - - +
159D VAL* 3.8 3.7 - - - -
160D ASP* 2.9 28.1 + - - -
163D ASN* 2.8 27.1 + - - +
165D PRO* 4.0 21.8 - - + -
168D LEU* 3.4 21.7 - - + +
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Residues in contact with ALA 79 (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* 3.6 34.3 - - + -
72D VAL* 4.6 4.5 - - + -
73D VAL 3.5 4.3 - - - +
74D GLN* 4.0 17.9 - - + +
77D ASP 4.0 0.6 + - - +
78D THR* 1.3 75.6 - - - +
80D VAL* 1.3 63.7 + - - +
156D LEU 3.8 0.3 - - - -
157D LEU* 3.0 31.9 + - + -
158D ALA* 2.8 17.7 + - + +
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Residues in contact with VAL 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D ALA 3.9 0.7 - - - +
72D VAL* 3.3 3.4 - - - +
73D VAL* 2.8 42.6 + - - +
78D THR* 4.5 1.6 - - + -
79D ALA* 1.3 78.6 - - - +
81D MET* 1.3 63.6 + - - +
82D VAL* 3.9 13.5 + - + +
154D CYS* 4.7 2.0 - - + -
155D ASN 3.6 6.3 - - - +
156D LEU* 3.7 25.1 - - + -
157D LEU* 4.5 1.8 - - - -
165D PRO* 3.8 27.1 - - + +
168D LEU* 3.9 15.5 - - + +
169D ALA* 3.8 29.2 - - + -
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Residues in contact with MET 81 (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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432C TYR* 3.5 38.8 - - + +
477C LEU* 4.3 11.9 - - + -
63D LEU* 3.6 34.8 - - + -
64D ALA* 4.0 11.7 - - + -
70D SER* 4.2 9.0 - - - +
71D ALA 3.3 13.2 - - - +
72D VAL* 4.2 4.3 - - + +
80D VAL* 1.3 74.2 - - - +
82D VAL* 1.3 64.7 + - - +
83D THR* 4.2 7.0 - - + -
153D LEU 3.9 0.3 - - - +
154D CYS* 3.3 2.6 - - - -
155D ASN* 2.7 55.9 + - + +
157D LEU* 3.9 20.2 - - + +
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Residues in contact with VAL 82 (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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70D SER* 3.4 2.6 + - - -
71D ALA 2.9 31.4 + - - +
80D VAL* 3.9 16.2 - - + +
81D MET* 1.3 81.2 - - - +
83D THR* 1.3 66.4 + - - +
152D VAL* 3.6 22.4 - - + -
153D LEU 3.2 5.4 - - - +
154D CYS* 4.0 11.9 - - - -
169D ALA 3.6 10.3 - - - +
172D GLY* 3.5 30.1 - - - +
173D ALA* 3.5 26.2 - - + +
176D ALA* 3.6 5.6 - - + +
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Residues in contact with THR 83 (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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432C TYR* 3.2 54.4 - - + +
64D ALA* 4.1 8.1 - - + -
67D ALA* 4.1 3.1 - - + -
69D GLY 3.2 8.7 - - - +
70D SER* 4.1 15.0 - - - +
81D MET* 4.2 11.0 - - + -
82D VAL* 1.3 78.6 - - - +
84D ALA* 1.3 60.8 + - - +
85D VAL* 4.4 1.6 - - - +
151D GLN 3.7 0.7 + - - +
152D VAL* 3.2 9.2 - - - +
153D LEU* 2.8 39.5 + - - +
176D ALA* 4.4 2.9 - - - -
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Residues in contact with ALA 84 (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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67D ALA* 4.1 0.2 - - - +
68D ASP* 3.3 8.8 + - - +
69D GLY 2.9 32.4 + - - +
83D THR* 1.3 74.2 - - - +
85D VAL* 1.3 65.9 + - - +
150D THR* 6.1 0.9 - - - +
151D GLN 3.5 5.4 - - - +
152D VAL* 4.5 6.5 - - + -
176D ALA* 4.3 14.6 - - + +
177D LEU* 4.0 24.0 - - + -
182D ILE* 3.9 18.6 - - + -
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Residues in contact with VAL 85 (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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432C TYR* 4.2 23.1 - - + -
435C ASN* 3.4 41.7 - - - +
436C GLU 3.7 22.9 - - - +
437C ILE* 3.6 16.6 - - + +
67D ALA* 4.2 3.8 - - + -
68D ASP* 3.5 4.0 - - - +
83D THR* 5.0 0.9 - - - +
84D ALA* 1.3 79.9 - - - +
86D SER* 1.3 65.7 + - - +
87D LYS* 5.0 2.5 - - + +
150D THR* 3.0 5.8 + - - -
151D GLN* 2.9 37.0 + - + +
153D LEU* 6.5 0.4 - - + -
182D ILE* 4.2 1.3 - - - +
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Residues in contact with SER 86 (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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435C ASN* 5.8 0.2 + - - -
68D ASP* 2.7 15.4 + - - +
85D VAL* 1.3 78.5 - - - +
87D LYS* 1.3 60.4 + - - +
88D THR* 3.7 2.9 + - - +
89D LYS* 4.9 0.3 + - - -
146D TYR* 2.7 29.1 + - - -
148D TYR* 4.1 0.5 - - - +
149D ASP 3.4 2.6 + - - -
150D THR* 3.0 25.3 - - - +
182D ILE* 3.5 22.4 - - - +
271D ARG* 2.7 27.4 + - - -
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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