Contacts of the strand formed by residues 89 - 94 (chain D) in PDB entry 4UC5
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 LEU 89 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55D ARG* 3.9 5.0 + - - -
56D LEU* 3.4 34.5 - - + +
58D VAL* 4.0 19.5 - - + -
82D ARG* 4.8 1.9 - - - +
85D TYR* 2.8 49.3 + - + +
86D GLU* 3.6 15.8 - - - +
87D ASN 3.9 0.2 - - - -
88D GLU* 1.3 84.0 - - + +
90D LEU* 1.3 59.9 + - - +
91D ILE* 3.8 21.5 + - + +
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Residues in contact with LEU 90 (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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41D THR* 4.4 8.1 - - + -
44D GLU* 3.5 43.1 - - + +
45D ILE* 3.8 22.0 - - + -
48D LEU* 4.1 16.4 - - + -
55D ARG* 4.0 20.9 - - + +
56D LEU 2.7 14.6 + - - +
57D LEU* 3.2 18.9 - - + +
58D VAL 2.9 24.0 + - - -
82D ARG* 3.5 26.7 - - - +
89D LEU* 1.3 70.6 - - - +
91D ILE* 1.3 60.4 + - - +
92D VAL* 4.5 2.5 - - + -
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Residues in contact with ILE 91 (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 VAL* 3.6 16.6 - - + -
60D ILE* 4.0 8.5 - - + -
78D LEU* 3.8 39.0 - - + -
81D LEU* 4.0 14.8 - - + +
82D ARG* 2.9 68.9 + - + +
85D TYR* 4.5 4.3 - - + -
89D LEU* 3.8 31.7 + - + +
90D LEU* 1.3 74.0 - - - +
92D VAL* 1.3 66.8 + - - +
140D MET* 4.4 1.5 - - - +
141D PRO* 4.2 1.2 - - - +
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Residues in contact with VAL 92 (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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41D THR* 4.1 23.8 - - + -
45D ILE* 4.5 3.4 - - + -
57D LEU* 3.9 19.5 - - + -
58D VAL 2.9 10.6 + - - +
59D ILE* 3.4 12.9 - - + -
60D ILE* 2.9 25.8 + - - +
90D LEU* 4.3 3.4 - - + +
91D ILE* 1.3 85.8 - - - +
93D MET* 1.3 65.7 + - - +
140D MET* 4.6 0.7 - - - -
141D PRO* 3.5 26.0 - - + +
142D ALA 3.8 17.3 - - - +
143D SER* 3.9 9.9 - - - +
160D SER* 5.0 3.8 - - - -
161D TRP* 5.1 2.0 - - + -
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Residues in contact with MET 93 (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 ILE 3.3 11.4 - - - +
61D GLY* 4.8 0.4 - - - -
62D PRO* 4.4 4.3 - - + -
65D ILE* 4.4 9.6 - - + -
71D ALA* 3.6 35.9 - - + +
74D TYR* 4.1 16.8 - - + -
75D ALA* 3.7 30.1 - - - -
78D LEU* 4.1 7.6 - - + -
92D VAL* 1.3 70.5 - - - +
94D ARG* 1.3 76.3 - - - +
95D VAL* 3.4 11.0 + - + +
135D LEU* 3.9 14.4 - - + -
140D MET* 3.8 14.4 - - + -
141D PRO 3.1 16.1 + - - +
142D ALA* 3.6 1.7 - - - -
143D SER* 2.8 29.4 + - - -
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Residues in contact with ARG 94 (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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59D ILE* 4.1 14.8 + - + +
60D ILE* 2.9 10.6 + - - +
61D GLY 3.4 25.8 - - - +
62D PRO* 2.7 40.2 - - - +
63D CYS* 3.0 32.1 + - - +
65D ILE* 4.3 1.9 - - - +
92D VAL 3.5 2.2 + - - -
93D MET* 1.3 78.7 - - - +
95D VAL* 1.3 59.5 + - - +
96D TYR* 3.2 53.3 + - + +
143D SER* 3.1 11.4 + - - +
188D LYS* 4.6 8.1 - - - +
267D ASP* 5.2 3.2 + - - -
270D HIS* 3.9 25.4 + - - -
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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