Contacts of the strand formed by residues 130 - 140 (chain D) 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 THR 130 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132C PHE* 6.0 0.3 - - - -
153C LYS* 4.9 16.8 + - - +
154C ASP* 5.4 1.0 + - - -
125D GLN* 2.9 49.1 + - - +
126D LEU* 3.8 3.3 + - - -
128D SER* 3.7 10.3 + - - +
129D GLY* 1.3 81.6 - - - +
131D ALA* 1.3 59.8 + - - +
181D THR* 6.5 0.7 - - - -
182D LEU 3.8 8.3 - - - +
183D SER* 5.0 3.8 - - - -
184D LYS* 4.4 1.3 - - - +
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Residues in contact with ALA 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D PRO* 3.8 23.1 - - + -
125D GLN* 3.5 3.4 - - - +
126D LEU* 4.0 9.2 - - + -
130D THR* 1.3 74.4 - - - +
132D SER* 1.3 59.6 + - - +
133D VAL* 5.1 1.9 - - + +
180D LEU 3.5 2.6 - - - +
181D THR* 3.6 1.4 - - - -
182D LEU* 2.7 46.0 + - + +
183D SER 4.6 1.8 - - - +
187D TYR* 3.8 30.1 - - + -
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Residues in contact with SER 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C LEU* 5.5 4.3 - - - +
151C LEU* 3.8 17.5 - - - +
153C LYS* 3.3 21.1 - - - +
119D PHE 4.4 0.9 - - - +
120D PRO 4.5 0.3 - - - -
121D PRO* 3.4 21.8 - - - +
125D GLN* 2.8 32.9 + - - +
131D ALA* 1.3 71.1 - - - +
133D VAL* 1.3 61.8 + - - +
134D ALA* 3.9 2.9 + - - +
179D THR* 3.9 15.9 - - - -
180D LEU 3.4 3.6 - - - -
181D THR* 3.4 7.4 - - - +
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Residues in contact with VAL 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D ILE* 4.2 4.7 - - + -
119D PHE 3.4 16.8 - - - +
121D PRO* 3.9 18.2 - - + -
131D ALA 5.1 1.6 - - - +
132D SER* 1.3 74.6 - - - +
134D ALA* 1.3 57.9 + - - +
149D TRP* 3.3 36.0 - - + -
179D THR* 3.4 2.2 - - - -
180D LEU* 3.0 41.5 + - + +
182D LEU* 5.6 2.2 - - + -
187D TYR* 4.7 9.4 - - + -
193D TYR* 4.7 13.0 - - + -
210D PHE* 3.7 26.9 - - + -
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Residues in contact with ALA 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C LEU* 3.9 30.5 - - + -
151C LEU* 4.5 13.7 - - + -
189C SER* 5.8 3.6 - - - -
118D ILE* 3.8 1.7 - - - +
119D PHE* 2.8 46.1 + - + +
132D SER 3.9 2.6 + - - +
133D VAL* 1.3 71.4 - - - +
135D CYS* 1.3 58.3 + - - +
136D LEU 4.1 0.4 - - - -
149D TRP* 4.3 0.9 - - - -
177D SER* 6.1 4.0 - - - -
178D SER 3.5 6.7 - - - +
179D THR* 4.6 6.1 - - - +
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Residues in contact with CYS 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D VAL* 3.9 17.5 - - - -
117D PHE 3.4 12.3 - - - -
118D ILE* 4.7 2.7 - - - +
134D ALA* 1.3 71.9 - - - +
136D LEU* 1.3 62.4 + - - +
137D LEU* 3.7 8.7 - - + +
149D TRP* 3.6 17.0 - - + -
176D LEU 3.5 1.4 - - - +
177D SER* 3.4 7.5 - - - +
178D SER* 2.9 33.1 + - - +
195D CYS* 2.0 50.0 - - - -
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Residues in contact with LEU 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C ALA* 3.7 19.7 - - + -
174C HIS* 5.8 1.1 - - + -
176C PHE* 3.7 29.2 - - + -
191C VAL* 3.9 27.6 - - + -
193C THR* 5.5 0.7 - - - +
116D VAL* 3.3 10.0 - - - +
117D PHE* 2.8 59.1 + - + +
119D PHE* 3.8 17.6 - - + -
134D ALA 4.1 1.4 + - - -
135D CYS* 1.3 72.7 - - - +
137D LEU* 1.3 62.5 + - - +
138D ASN* 3.8 30.3 - - + +
176D LEU 3.6 1.6 - - - -
177D SER* 4.8 2.5 - - - +
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Residues in contact with LEU 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D PRO* 4.2 9.9 - - + -
115D SER 3.9 4.3 - - - -
116D VAL* 4.6 1.3 - - + -
135D CYS* 3.7 17.5 - - - +
136D LEU* 1.3 80.1 - - - +
138D ASN* 1.3 60.1 + - - +
140D PHE* 3.2 26.5 - - + -
145D ALA* 4.3 16.4 - - + -
147D VAL* 3.8 28.9 - - + -
175D SER* 3.3 3.2 - - - -
176D LEU* 2.8 43.4 + - + +
197D VAL* 3.7 41.3 - - + -
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Residues in contact with ASN 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C HIS* 3.3 29.7 + - - -
193C THR* 3.0 33.7 + - - +
115D SER* 3.0 42.2 + - - +
117D PHE* 5.1 3.0 - - + -
136D LEU* 3.8 26.0 - - + +
137D LEU* 1.3 72.0 - - - +
139D ASN* 1.4 89.1 + - - +
175D SER* 3.6 8.7 + - - -
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Residues in contact with ASN 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C HIS* 3.8 21.7 + - - -
193C THR* 6.0 0.2 - - - -
112D ALA* 4.7 3.6 - - - +
113D ALA 3.5 13.0 - - - +
138D ASN* 1.4 101.7 + - - +
140D PHE* 1.3 59.9 + - - +
168D ASP* 5.2 0.2 - - - -
171D ASP* 3.4 20.1 + - - +
173D THR* 2.9 30.3 + - + +
174D TYR 3.4 5.3 + - - -
175D SER* 3.4 10.4 + - - -
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Residues in contact with PHE 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D ALA* 3.6 15.0 - - - +
114D PRO* 3.7 25.6 - - + -
137D LEU* 3.2 35.2 - - + -
139D ASN* 1.3 73.5 - - - +
141D TYR* 1.3 61.9 + - - +
142D PRO 3.2 26.7 - - - -
143D ARG* 3.5 21.3 - - - -
145D ALA* 3.9 16.4 - - + -
164D VAL* 4.9 2.2 - - + -
173D THR* 3.5 8.4 - - - -
174D TYR* 2.8 57.2 + - + -
175D SER 4.4 0.4 - - - -
176D LEU* 3.6 29.2 - - + -
199D HIS* 3.4 11.4 - + - +
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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