Contacts of the strand formed by residues 150 - 158 (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 150 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437C ILE* 3.6 2.6 - - - +
84D ALA* 6.1 0.9 - - - +
85D VAL 3.0 14.0 + - - -
86D SER* 3.0 24.0 - - - +
96D MET* 3.8 20.6 - - + -
97D PRO 2.9 7.2 + - - +
98D LEU* 3.5 19.5 - - - +
99D VAL* 3.1 26.0 + - - +
142D PHE* 4.4 9.4 - - + -
146D TYR* 3.9 5.4 - - + -
148D TYR 2.6 27.6 - - - +
149D ASP* 1.3 71.6 + - - +
151D GLN* 1.3 61.4 + - - +
152D VAL* 5.2 2.3 - - - +
177D LEU* 5.4 3.1 - - - +
182D ILE* 5.4 1.4 - - - +
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Residues in contact with GLN 151 (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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431C PRO* 3.8 2.3 - - - +
436C GLU 4.4 0.7 - - - +
437C ILE* 3.5 22.5 - - + +
438C GLY 3.0 43.2 + - - +
440C VAL* 5.2 1.2 - - - +
83D THR* 3.7 1.6 + - - +
84D ALA* 3.5 2.3 - - - -
85D VAL* 2.9 33.9 + - + +
99D VAL* 3.3 21.3 - - + +
101D ASP* 2.9 24.6 + - - +
150D THR* 1.3 76.0 + - - +
152D VAL* 1.3 67.2 + - - +
153D LEU* 3.8 32.9 + - + +
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Residues in contact with VAL 152 (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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82D VAL* 3.6 27.1 - - + -
83D THR 3.2 6.3 - - - +
84D ALA* 4.5 11.9 - - + -
98D LEU* 4.6 7.2 - - + -
99D VAL 2.9 6.5 + - - +
100D VAL* 3.4 23.4 - - + +
101D ASP* 2.8 28.1 + - - +
134D ILE* 4.7 0.9 - - + -
138D ILE* 3.8 23.6 - - + -
150D THR* 5.2 2.0 - - - +
151D GLN* 1.3 77.6 - - - +
153D LEU* 1.3 64.1 + - - +
154D CYS* 4.6 3.6 - - - -
173D ALA* 3.9 13.5 - - + -
177D LEU* 4.7 9.6 - - + -
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Residues in contact with LEU 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430C PRO* 6.1 0.2 - - + -
431C PRO* 3.7 26.5 - - + -
432C TYR* 3.7 31.2 - - + +
440C VAL* 4.0 23.1 - - + -
81D MET 3.9 0.5 - - - +
82D VAL* 3.2 4.7 - - - +
83D THR* 2.8 44.9 + - - +
85D VAL* 6.5 0.7 - - + -
101D ASP* 3.4 33.2 - - + +
103D ARG* 4.6 6.5 - - - +
151D GLN* 3.8 23.7 + - + +
152D VAL* 1.3 75.3 - - - +
154D CYS* 1.3 64.7 + - - +
155D ASN 4.2 0.2 + - - -
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Residues in contact with CYS 154 (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* 6.1 0.4 - - - -
80D VAL* 4.7 3.8 - - + -
81D MET 3.3 6.7 - - - +
82D VAL* 4.0 22.7 - - + -
100D VAL* 4.9 0.9 - - - -
101D ASP 3.1 8.7 + - - +
102D TYR* 3.9 31.0 - - + -
103D ARG* 3.7 28.5 + - - +
134D ILE* 3.9 27.4 - - - -
152D VAL* 4.6 6.7 - - - -
153D LEU* 1.3 78.4 - - - +
155D ASN* 1.3 59.7 + - - +
156D LEU* 5.1 0.9 - - + -
169D ALA* 4.0 6.3 - - + -
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Residues in contact with ASN 155 (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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394C LEU* 5.1 0.2 - - - +
432C TYR* 3.5 22.2 + - + +
475C GLU* 2.9 30.2 + - - -
477C LEU* 4.4 8.3 - - - +
80D VAL* 3.6 1.4 - - - +
81D MET* 2.7 57.0 + - + +
103D ARG 4.9 0.2 - - - -
105D LYS* 2.7 27.4 + - - +
153D LEU 4.2 0.6 + - - -
154D CYS* 1.3 73.2 - - - +
156D LEU* 1.3 64.7 + - - +
157D LEU* 3.2 16.8 + - - +
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Residues in contact with LEU 156 (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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79D ALA 4.0 4.9 - - - +
80D VAL* 3.7 25.4 - - + -
102D TYR* 3.6 39.7 - - + +
103D ARG 3.5 18.1 + - - +
104D GLN* 3.9 24.7 - - + +
105D LYS* 3.1 29.7 + - + +
154D CYS* 4.1 1.1 - - + -
155D ASN* 1.3 73.8 + - - +
157D LEU* 1.3 64.7 + - - +
158D ALA* 3.3 1.8 + - - -
159D VAL* 3.9 24.9 - - + +
165D PRO* 3.8 15.3 - - + -
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Residues in contact with LEU 157 (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* 3.8 34.7 - - + -
380C LEU* 3.5 23.0 - - - +
394C LEU* 3.9 24.1 - - + +
396C THR* 4.8 2.1 + - - -
477C LEU* 5.4 1.3 - - + -
63D LEU* 4.0 21.8 - - + -
72D VAL* 4.3 15.7 - - + -
79D ALA* 3.0 12.6 + - + +
81D MET* 3.9 29.6 - - + +
105D LYS* 4.1 5.8 + - - +
155D ASN* 3.2 28.2 + - - +
156D LEU* 1.3 74.3 - - - +
158D ALA* 1.3 62.6 + - - +
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Residues in contact with ALA 158 (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* 3.9 33.4 - - + -
379C THR* 4.5 5.2 - - - -
380C LEU* 4.0 13.5 - - + -
77D ASP 3.9 13.0 - - - +
78D THR* 3.4 3.1 - - - +
79D ALA 2.8 29.4 + - - +
80D VAL* 5.3 0.2 - - - +
156D LEU* 3.3 0.8 - - - +
157D LEU* 1.3 82.2 - - - +
159D VAL* 1.3 68.1 + - - +
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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