Contacts of the strand formed by residues 168 - 175 (chain B) in PDB entry 1UMZ
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 LYS 168 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B GLN* 3.9 21.1 - - + +
47B SER* 3.5 28.0 - - - +
48B LYS 3.8 14.9 + - - -
49B GLY 3.5 7.4 - - - +
50B SER* 3.3 24.3 + - - +
76B LEU* 3.2 5.1 - - - -
77B SER 3.0 29.8 + - - -
79B GLN* 4.3 13.7 + - - +
167B MET* 1.3 72.4 - - - +
169B ILE* 1.3 64.0 + - - +
170B TYR* 3.5 31.5 - - + +
211B VAL* 5.4 3.6 - - - +
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Residues in contact with ILE 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B TYR* 3.2 32.3 - - + +
46B GLN* 3.1 6.8 - - - +
47B SER* 2.8 41.6 + - - +
51B TYR* 3.5 34.8 - - + -
56B PHE* 3.8 28.9 - - + -
58B MET* 5.1 0.7 - - + -
74B PHE* 3.7 26.9 - - + -
75B TYR 3.5 6.3 - - - +
76B LEU* 4.0 12.8 - - + -
167B MET 4.6 1.6 - - - +
168B LYS* 1.3 75.5 - - - +
170B TYR* 1.3 64.1 + - - +
204B ILE* 4.0 4.9 - - + -
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Residues in contact with TYR 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B THR* 4.9 5.6 - - + -
45B PHE* 3.4 9.0 - - - +
46B GLN* 3.6 35.7 + - + -
74B PHE* 3.4 2.9 - - - -
75B TYR* 2.7 78.3 + + + +
77B SER* 3.8 17.9 - - - -
78B SER 5.0 0.3 + - - -
79B GLN* 3.0 24.4 + - - +
168B LYS* 3.5 39.1 - - + +
169B ILE* 1.3 74.5 - - - +
171B SER* 1.3 67.2 + - - +
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Residues in contact with SER 171 (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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35B LEU* 4.6 1.1 - - - -
44B GLY* 3.0 2.9 - - - -
45B PHE* 2.8 67.4 + - - +
58B MET* 3.6 11.8 - - - +
73B ALA 3.1 14.8 - - - -
74B PHE* 3.7 5.7 - - - -
75B TYR* 4.8 1.3 - - - -
170B TYR* 1.3 78.3 + - - +
172B SER* 1.3 63.2 + - - +
199B TYR* 3.6 18.3 - - - -
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Residues in contact with SER 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LEU* 4.1 6.5 - - - -
43B THR 3.3 13.7 - - - -
44B GLY* 3.9 3.6 - - - -
71B VAL 3.8 0.2 - - - +
72B THR* 3.4 2.9 - - - -
73B ALA* 2.8 43.0 + - - +
75B TYR* 4.2 11.0 + - - -
171B SER* 1.3 79.2 - - - +
173B LEU* 1.3 61.0 + - - +
174B TRP* 3.3 24.4 + - - -
199B TYR* 3.9 3.0 + - - -
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Residues in contact with LEU 173 (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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35B LEU* 3.5 32.5 - - + +
37B LEU* 3.6 27.1 - - + +
42B GLY* 3.2 7.7 - - - -
43B THR* 2.9 28.9 + - + +
63B VAL* 4.3 10.5 - - + -
70B THR* 4.4 5.4 - - - -
71B VAL 3.4 11.7 - - - +
72B THR* 3.3 25.6 - - + +
172B SER* 1.3 74.4 - - - +
174B TRP* 1.3 62.1 + - - +
195B PHE 3.2 30.5 - - - +
196B ILE 4.6 0.2 - - - -
197B ALA* 4.1 10.3 - - + +
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Residues in contact with TRP 174 (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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242A TRP* 6.3 2.9 - - + -
246A LYS* 4.6 15.5 - - - +
37B LEU* 3.8 13.8 - - - +
42B GLY* 4.8 3.1 - - - +
70B THR* 3.6 2.6 - - - -
71B VAL* 2.9 63.9 + - + +
73B ALA* 4.1 7.0 - - + +
75B TYR* 6.1 0.2 - - - -
89B GLU* 4.0 11.9 - - - -
172B SER* 3.3 29.1 + - - -
173B LEU* 1.3 77.0 - - - +
175B ASN* 1.3 81.8 + - - +
176B ALA* 3.7 10.5 - - + -
179B TRP* 3.9 15.7 - + - -
3F BGC 3.9 11.2 - - - -
4F XYS 3.2 32.3 - - - -
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Residues in contact with ASN 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 4.0 8.4 - - + +
69B GLY 3.4 5.0 - - - +
70B THR* 4.6 0.4 - - - +
174B TRP* 1.3 91.4 - - - +
176B ALA* 1.3 62.2 + - - +
177B ASP* 2.9 28.4 + - - +
188B THR* 2.6 31.2 + - - -
190B TRP* 3.7 30.0 - - + +
4F XYS 5.2 0.2 + - - -
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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