Contacts of the strand formed by residues 136 - 143 (chain B) in PDB entry 3UAJ
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 GLU 136 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B LYS* 3.6 3.8 + - - +
48B THR* 3.5 3.4 - - - -
49B THR* 2.8 49.6 + - + +
51B LYS* 4.2 32.6 + - + +
134B ASN 4.4 0.2 - - - -
135B LEU* 1.3 70.3 - - - +
137B TYR* 1.3 63.7 + - - +
138B THR* 3.8 4.3 + - - +
163B MET* 3.4 49.3 - - + +
164B ILE 3.6 1.8 - - - +
165B THR* 3.9 17.1 + - + +
54C ARG* 6.1 0.2 - - - +
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Residues in contact with TYR 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B LEU* 3.9 19.7 - - + -
47B LYS 3.7 3.6 - - - -
48B THR* 3.3 33.6 - - + +
132B ILE* 5.5 1.2 - - - +
135B LEU* 3.7 35.7 - - + +
136B GLU* 1.3 71.5 - - - +
138B THR* 1.3 60.6 + - - +
139B VAL* 3.9 0.8 + - - -
162B ALA 3.3 5.0 - - - +
163B MET* 3.4 2.2 - - - -
164B ILE* 2.7 60.5 + - + +
165B THR* 5.1 0.2 - - - -
166B PRO* 4.9 1.3 - - + -
187B PRO* 3.5 35.3 - - + +
188B ARG 5.0 1.2 + - - -
189B SER* 5.2 8.3 - - - -
281B GLY 6.4 1.6 - - - -
282B HIS 5.6 3.3 + - - -
283B LEU* 3.7 28.5 - - + -
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Residues in contact with THR 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B LEU* 3.6 5.6 - - - +
46B THR* 2.9 34.2 + - + -
47B LYS* 2.8 48.0 + - + +
136B GLU* 4.2 5.5 + - - +
137B TYR* 1.3 72.3 - - - +
139B VAL* 1.3 62.6 + - - +
140B VAL* 5.1 0.7 - - + -
161B THR* 4.3 24.0 - - + -
162B ALA 3.4 9.0 - - - +
163B MET* 4.6 16.4 - - + +
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Residues in contact with VAL 139 (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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25B LEU* 3.9 23.1 - - + -
43B PHE* 4.2 20.0 - - + -
44B GLU 3.5 12.1 - - - +
45B LEU* 3.8 20.4 - - + -
137B TYR 4.6 0.9 - - - +
138B THR* 1.3 75.8 - - - +
140B VAL* 1.3 64.1 + - - +
141B VAL* 4.1 1.4 + - + +
160B VAL 3.7 1.4 - - - +
161B THR* 3.5 1.6 - - - -
162B ALA* 2.8 40.9 + - - +
164B ILE* 3.8 20.2 - - + -
183B LEU* 4.3 16.6 - - + -
283B LEU* 3.9 12.1 - - + -
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Residues in contact with VAL 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B ARG* 3.6 40.2 - - - +
42B ASP 3.1 13.3 - - - +
43B PHE* 3.5 1.7 - - - -
44B GLU* 2.9 27.9 + - - +
46B THR* 3.3 28.9 - - + +
138B THR* 5.1 2.5 - - + -
139B VAL* 1.3 74.9 - - - +
141B VAL* 1.3 61.3 + - - +
142B THR* 3.7 8.2 + - - +
159B GLY* 4.5 3.4 - - - +
160B VAL 3.5 14.6 - - - +
161B THR* 3.8 24.5 - - + -
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Residues in contact with VAL 141 (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 LEU* 3.9 26.9 - - + -
42B ASP 3.4 3.6 - - - +
43B PHE* 3.7 37.0 - - + -
139B VAL* 4.1 2.0 + - + +
140B VAL* 1.3 69.0 - - - +
142B THR* 1.3 63.7 + - - +
143B VAL* 5.3 0.2 - - - +
159B GLY* 3.6 1.2 - - - -
160B VAL* 2.9 42.9 + - + +
162B ALA* 6.0 1.3 - - + -
173B VAL* 3.9 23.6 - - + -
175B LEU* 3.9 28.3 - - + +
181B LEU* 4.4 2.5 - - + -
183B LEU* 6.5 0.4 - - + -
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Residues in contact with THR 142 (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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1B MET 4.5 5.4 - - - +
2B ARG* 3.2 44.7 + - + +
41B LEU* 3.5 3.1 - - - -
42B ASP* 2.7 42.0 + - - +
140B VAL* 3.7 7.8 - - - +
141B VAL* 1.3 75.2 + - - +
143B VAL* 1.3 73.0 + - - +
145B ASN* 5.4 1.6 - - - +
158B HIS 4.0 27.6 - - - +
159B GLY* 3.8 5.2 - - - -
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Residues in contact with VAL 143 (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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1B MET 3.4 12.1 + - - -
39B PRO* 4.4 4.7 - - + -
40B THR 3.8 11.9 - - - +
41B LEU* 3.8 20.9 - - + -
142B THR* 1.3 79.6 - - - +
144B HIS* 1.3 66.3 + - - +
145B ASN* 3.0 20.5 - - - +
175B LEU* 4.0 19.7 - - + -
178B TYR* 3.5 55.9 - - + +
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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