Contacts of the strand formed by residues 56 - 64 (chain B) in PDB entry 1UWB
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 TYR 56 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17B ASP* 3.9 12.4 + - - -
18B GLY* 3.7 17.0 - - - -
19B PRO 3.1 11.4 - - - +
20B LYS* 3.4 32.8 - - + -
54B ASN* 2.8 13.9 + - - -
55B PRO* 1.3 80.3 - - + +
57B ASN* 1.3 64.9 + - - +
126B LYS* 3.1 55.2 + - + +
127B TYR* 3.1 46.7 + + - +
129B ALA* 3.1 13.0 - - + +
143B ARG* 2.7 29.6 + - - -
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Residues in contact with ASN 57 (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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88A TRP* 3.9 16.0 - - + -
19B PRO 2.9 7.8 + - - +
20B LYS* 4.1 1.7 - - - +
21B VAL* 2.9 49.9 + - - +
22B LYS 4.5 0.2 - - - -
23B GLN* 3.8 28.3 - - - +
56B TYR* 1.3 82.1 - - - +
58B THR* 1.3 77.4 + - - +
129B ALA 3.1 6.3 - - - -
130B PHE* 2.9 12.0 - - - -
131B THR* 2.6 40.7 + - - +
143B ARG* 3.5 0.3 + - - -
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Residues in contact with THR 58 (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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19B PRO* 3.6 19.0 - - + +
21B VAL* 3.9 4.7 - - + -
57B ASN* 1.3 87.0 + - - +
59B PRO* 1.3 71.2 - - + +
60B VAL* 3.7 2.4 - - - +
75B VAL* 3.7 13.0 - - + +
76B ASP 2.8 34.5 - - - +
77B PHE* 3.9 19.6 - - + +
79B GLU 5.5 0.4 - - - +
80B LEU* 5.0 5.5 - - + +
127B TYR 4.0 5.4 + - - -
128B THR 5.8 0.4 - - - -
129B ALA 2.8 13.2 + - - -
130B PHE* 3.5 21.4 - - - +
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Residues in contact with PRO 59 (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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21B VAL* 3.3 36.6 - - + -
22B LYS 4.3 10.3 - - - +
23B GLN* 3.1 15.3 - - - +
24B TRP* 4.6 9.9 - - + +
57B ASN* 4.6 0.4 - - - -
58B THR* 1.3 93.8 - - + +
60B VAL* 1.3 57.1 + - - +
61B PHE* 3.8 11.2 - - + -
75B VAL* 2.9 11.1 - - - +
76B ASP* 2.6 53.2 + - + +
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Residues in contact with VAL 60 (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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23B GLN* 3.0 21.7 + - - +
26B LEU* 3.9 4.8 - - + +
34B LEU* 4.1 27.6 - - + -
58B THR 3.7 8.5 - - - +
59B PRO* 1.3 79.9 - - - +
61B PHE* 1.3 79.2 + - - +
73B LYS* 4.8 9.0 - - + -
74B LEU 3.0 11.0 - - - +
75B VAL* 4.1 10.3 - - + -
130B PHE* 4.1 17.9 - - + -
131B THR 3.4 25.8 - - - +
132B ILE* 5.4 4.7 - - + -
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Residues in contact with PHE 61 (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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24B TRP* 4.1 25.1 - + + -
26B LEU* 4.3 16.4 - - + -
34B LEU* 4.2 1.5 - - - +
59B PRO* 3.8 11.4 - - + -
60B VAL* 1.3 88.1 - - - +
62B ALA* 1.3 63.5 + - - +
63B ILE* 4.6 2.9 - - + -
72B ARG 3.5 0.3 - - - +
73B LYS* 3.6 2.1 - - - -
74B LEU* 2.7 56.8 + - + +
76B ASP* 3.2 41.5 - - + -
78B ARG* 5.7 1.3 - - - -
402B TRP* 3.6 41.7 - + + -
403B THR* 3.9 19.3 - - + +
411B ILE* 4.3 1.6 - - + -
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Residues in contact with ALA 62 (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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30B LYS* 3.3 42.4 + - + +
33B ALA* 4.5 1.8 - - + -
34B LEU* 3.9 23.6 - - + +
61B PHE* 1.3 70.1 - - - +
63B ILE* 1.3 64.9 + - - +
71B TRP* 3.2 32.8 - - + -
72B ARG 3.4 6.1 - - - +
403B THR* 3.8 7.8 + - - +
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Residues in contact with ILE 63 (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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30B LYS* 5.1 0.2 - - - +
61B PHE* 3.7 4.3 - - + +
62B ALA* 1.3 81.2 - - - +
64B LYS* 1.3 61.4 + - - +
65B LYS* 4.0 27.4 - - + +
71B TRP* 3.2 5.3 - - - -
72B ARG* 2.5 56.4 + - + +
73B LYS 6.0 0.2 - - - +
74B LEU* 3.6 33.2 - - + -
403B THR* 4.9 7.4 - - - +
406B TRP* 3.8 24.2 - - + +
407B GLN* 4.3 0.9 - - - -
408B ALA 3.8 22.4 - - - +
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Residues in contact with LYS 64 (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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29B GLU* 4.2 12.7 + - - -
63B ILE* 1.3 71.0 - - - +
65B LYS* 1.3 64.8 + - - +
68B SER* 3.5 39.7 + - - +
69B THR 3.3 20.2 - - - +
71B TRP* 3.1 54.4 - - + +
404B GLU* 5.7 9.2 + - - +
406B TRP 5.4 0.9 + - - +
407B GLN* 3.7 12.3 - - - +
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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