Contacts of the strand formed by residues 89 - 94 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B ARG* 3.9 3.0 + - - -
56B LEU* 3.5 24.9 - - + +
58B VAL* 4.3 9.0 - - + -
82B ARG* 4.6 2.3 - - - +
85B TYR* 2.7 51.5 + - + +
86B GLU* 3.3 18.5 - - - +
87B ASN 3.7 0.2 - - - -
88B GLU* 1.3 84.8 - - + +
90B LEU* 1.3 59.6 + - - +
91B ILE* 3.7 14.0 + - + +
336B LEU* 3.8 38.1 - - + +
339B LEU* 3.9 25.6 - - + +
340B ALA* 3.9 6.5 - - + +
343B ASN* 4.6 0.9 - - + -
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Residues in contact with LEU 90 (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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41B THR* 4.6 8.3 - - + +
44B GLU* 3.4 39.5 - - + +
45B ILE* 3.7 31.0 - - + -
48B LEU* 4.1 21.5 - - + -
55B ARG* 3.7 22.2 - - + +
56B LEU 3.0 11.2 + - - +
57B LEU* 3.4 11.4 - - + +
58B VAL 3.0 23.3 + - - -
82B ARG* 3.7 24.9 - - - +
89B LEU* 1.3 70.3 - - - +
91B ILE* 1.3 57.8 + - - +
92B VAL* 4.6 3.6 - - + -
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Residues in contact with ILE 91 (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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58B VAL* 3.6 18.4 - - + -
60B ILE* 3.9 10.3 - - + -
78B LEU* 3.7 33.9 - - + -
81B LEU* 3.7 11.9 - - + +
82B ARG* 2.9 69.8 + - + +
85B TYR* 4.3 2.2 - - + -
89B LEU* 3.7 26.0 + - + +
90B LEU* 1.3 73.5 - - - +
92B VAL* 1.3 62.0 + - - +
140B MET* 4.4 1.2 - - + +
141B PRO* 4.4 1.0 - - - +
336B LEU* 4.2 21.5 - - + -
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Residues in contact with VAL 92 (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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41B THR* 4.1 24.7 - - + -
45B ILE* 4.4 4.3 - - + -
57B LEU* 4.0 18.6 - - + -
58B VAL 2.8 18.1 + - - +
59B ILE* 3.3 14.4 - - + -
60B ILE* 3.0 16.3 + - - +
82B ARG* 4.8 0.2 - - - +
90B LEU* 4.3 5.2 - - + +
91B ILE* 1.3 82.2 - - - +
93B MET* 1.3 63.9 + - - +
140B MET* 4.7 0.4 - - - -
141B PRO* 3.6 20.0 - - + +
142B ALA 3.8 22.9 - - - +
143B SER* 3.9 11.0 - - - -
160B SER* 5.2 1.6 - - - -
161B TRP* 5.0 3.1 - - + -
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Residues in contact with MET 93 (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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60B ILE 3.3 11.7 - - - +
61B GLY* 4.8 0.2 - - - -
62B PRO* 4.2 9.0 - - + -
65B ILE* 4.3 4.5 - - + -
71B ALA* 3.6 35.2 - - + +
74B TYR* 3.9 17.3 - - + -
75B ALA* 3.9 16.8 - - - -
78B LEU* 4.1 7.6 - - + -
92B VAL* 1.3 72.1 - - - +
94B ARG* 1.3 76.2 + - - +
95B VAL* 3.4 9.2 + - + +
135B LEU* 3.8 28.0 - - + -
140B MET* 3.8 14.9 - - + -
141B PRO 3.0 17.7 + - - +
142B ALA* 3.5 0.2 - - - -
143B SER* 2.8 30.1 + - - -
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Residues in contact with ARG 94 (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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59B ILE* 3.7 18.8 - - + -
60B ILE 2.9 9.2 + - - +
61B GLY* 3.6 25.4 - - - +
62B PRO* 2.3 50.9 + - - +
63B CYS* 2.6 27.8 + - - +
65B ILE* 4.2 1.6 - - - +
92B VAL 3.7 0.6 + - - -
93B MET* 1.3 79.9 - - - +
95B VAL* 1.3 62.9 + - - +
96B TYR* 3.3 53.1 + - + -
143B SER* 3.5 4.7 + - - -
188B LYS* 5.7 0.4 - - - +
270B HIS* 4.4 9.7 + - - -
302B MET* 4.6 10.9 - - - -
303B VAL 4.0 12.3 - - - -
304B GLU* 3.2 24.6 + - - +
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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