Contacts of the strand formed by residues 169 - 173 (chain B) in PDB entry 3UGV
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 GLY 169 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B ALA 4.4 0.4 + - - -
138B TYR* 3.2 18.4 - - - +
139B ASN 3.1 18.4 + - - -
167B PHE* 3.2 4.7 - - - +
168B LYS* 1.3 82.2 - - - +
170B LEU* 1.3 70.0 + - - +
197B THR* 4.2 1.3 - - - -
198B ALA* 3.2 17.7 - - - -
200B MET* 4.3 1.3 - - - -
322B TRP* 3.9 7.8 - - - -
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Residues in contact with LEU 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B TYR* 4.1 4.5 - - - +
139B ASN* 3.7 15.0 - - + +
143B LEU* 4.3 12.3 - - + -
155B ALA* 4.0 31.6 - - + +
158B LEU* 3.8 26.5 - - + -
159B LYS* 3.8 16.4 - - + +
167B PHE* 4.5 2.7 - - + -
169B GLY* 1.3 82.5 - - - +
171B LYS* 1.3 61.2 + - - +
172B LEU 3.6 0.7 + - - -
189B VAL* 4.6 0.7 - - + -
193B VAL* 4.4 11.0 - - + -
197B THR* 3.9 20.9 - - + -
198B ALA 2.8 10.5 + - - +
199B LEU* 3.3 16.4 - - + +
200B MET* 2.9 22.7 + - - -
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Residues in contact with LYS 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B TYR* 3.2 30.9 + - + -
139B ASN 3.0 17.9 + - - +
140B SER* 4.0 8.1 - - - -
142B GLY 3.3 19.9 - - - +
143B LEU* 3.4 9.5 - - - +
170B LEU* 1.3 70.4 - - - +
172B LEU* 1.3 62.7 + - - +
173B ARG* 3.8 33.6 + - - +
200B MET* 3.3 16.6 - - - +
202B ASP* 3.7 19.7 + - + +
228B GLU* 2.9 37.2 + - - -
275B MET* 3.9 2.0 - - - +
304B HIS* 5.2 0.4 - - - -
324B GLU* 3.0 23.2 + - - -
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Residues in contact with LEU 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B LEU* 3.9 17.5 - - + +
151B VAL* 4.0 15.5 - - + -
170B LEU 3.6 1.8 + - - +
171B LYS* 1.3 73.0 - - - +
173B ARG* 1.3 75.3 + - - +
174B MET* 3.9 16.6 + - + -
176B ARG* 5.2 0.7 - - - +
182B ASP 5.0 0.7 - - - +
185B THR* 3.9 24.2 - - + -
186B ALA* 3.8 36.3 - - + +
189B VAL* 4.7 2.9 - - + -
199B LEU* 4.4 19.1 - - + -
200B MET 2.8 9.6 + - - +
201B VAL* 3.2 15.9 - - + +
202B ASP 3.1 20.1 + - - -
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Residues in contact with ARG 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B SER* 2.9 42.2 + - - +
142B GLY* 2.5 40.2 + - - -
143B LEU 3.1 16.6 + - - +
144B TRP* 3.6 57.0 - - + -
145B LEU* 3.5 19.0 - - + +
171B LYS* 3.8 22.6 + - - +
172B LEU* 1.3 83.9 - - - +
174B MET* 1.3 65.6 + - - +
176B ARG* 3.6 8.0 + - - -
202B ASP* 3.5 8.8 + - + +
204B ASN* 3.7 16.6 - - - +
324B GLU* 5.1 2.2 + - - -
328B TRP* 4.3 6.5 - - - -
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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
------------------------------------------------------------
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