Contacts of the strand formed by residues 134 - 144 (chain B) in PDB entry 1UB5
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 134 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A LYS* 6.5 0.4 - - - -
129B GLN* 3.2 26.2 + - - +
130B LEU* 3.1 18.9 - - - +
132B SER* 3.3 7.1 + - - -
133B GLY* 1.3 80.3 - - - +
135B ALA* 1.3 65.5 + - - +
186B LEU 4.6 2.5 - - - -
187B THR* 5.3 0.4 - - - -
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Residues in contact with ALA 135 (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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125B PRO* 4.1 7.6 - - + -
129B GLN* 3.8 7.5 - - - +
130B LEU* 3.8 7.6 - - + -
134B GLY* 1.3 77.1 - - - +
136B SER* 1.3 61.1 + - - +
137B VAL 4.4 0.2 + - - -
185B THR* 5.1 2.3 - - - +
186B LEU* 2.7 62.6 + - + +
188B LYS* 3.6 16.6 - - - -
191B TYR* 3.8 11.2 - - + -
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Residues in contact with SER 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A LEU* 3.1 29.9 - - - +
146A LYS* 5.4 3.6 - - - -
124B PRO 4.2 0.9 - - - +
125B PRO* 3.5 22.9 - - - +
129B GLN* 3.1 18.9 + - - +
135B ALA* 1.3 73.5 - - - +
137B VAL* 1.3 61.3 + - - +
138B VAL* 4.0 3.1 + - - +
183B THR* 4.0 10.2 - - - +
184B LEU 3.3 5.2 - - - -
185B THR* 3.8 24.7 - - - -
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Residues in contact with VAL 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ILE* 4.0 4.9 - - + -
123B PHE 3.2 18.2 - - - +
124B PRO* 4.4 0.2 - - + -
125B PRO* 4.6 8.3 - - + -
136B SER* 1.3 74.7 - - - +
138B VAL* 1.3 60.1 + - - +
153B TRP* 3.2 36.0 - - + -
183B THR* 3.4 5.4 - - - -
184B LEU* 2.9 49.9 + - + +
186B LEU* 6.1 0.2 - - - +
191B TYR* 6.0 1.1 - - + -
197B TYR* 4.8 10.1 - - + -
214B PHE* 3.6 29.2 - - + -
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Residues in contact with VAL 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A LEU* 4.2 28.5 - - + -
181A SER* 4.6 5.8 - - - +
122B ILE* 3.3 2.5 - - - +
123B PHE* 2.5 52.1 + - + +
136B SER* 4.0 2.9 + - - +
137B VAL* 1.3 79.0 - - - +
139B CYS* 1.3 64.5 + - - +
140B PHE* 3.8 34.3 - - + -
181B SER* 5.0 1.3 - - - -
182B SER 3.6 3.8 - - - +
183B THR* 3.7 28.0 - - + +
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Residues in contact with CYS 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B VAL* 4.9 1.6 - - + -
121B SER 2.9 14.4 - - - +
122B ILE* 3.6 13.2 - - + -
123B PHE* 4.7 0.2 - - - -
138B VAL* 1.3 79.9 - - - +
140B PHE* 1.3 63.8 + - - +
141B LEU* 3.8 3.6 - - - +
153B TRP* 3.3 22.4 - - - -
181B SER* 3.7 1.2 - - - -
182B SER* 3.1 32.6 + - - -
199B CYS* 2.0 49.4 - - - -
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Residues in contact with PHE 140 (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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127A ALA* 5.5 3.8 - - + -
140A THR* 4.1 8.3 - - + -
141A LEU 4.7 2.7 - - - -
142A GLY* 4.8 4.7 - - - -
143A CYS 5.7 0.4 - - - -
169A PHE* 3.5 22.4 - + - -
181A SER* 3.3 32.8 - - - -
182A SER 4.4 2.9 - - - -
183A SER* 3.3 35.0 - - - -
119B THR 3.0 14.5 - - - +
120B VAL* 3.1 3.5 - - - -
121B SER* 2.8 26.6 + - - +
123B PHE* 3.9 29.2 - + - -
138B VAL* 3.8 15.0 - - + -
139B CYS* 1.3 71.8 - - - +
141B LEU* 1.3 65.4 + - - +
142B ASN* 3.3 19.7 - - - +
180B MET 3.6 2.2 - - - -
181B SER* 3.6 13.7 - - - -
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Residues in contact with LEU 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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118B PRO* 4.0 15.9 - - + -
119B THR 3.9 3.4 - - - -
120B VAL* 4.2 9.2 - - + -
139B CYS* 3.8 12.6 - - - +
140B PHE* 1.3 79.9 - - - +
142B ASN* 1.3 60.0 + - - +
144B PHE* 3.1 11.8 - - + -
149B ILE* 3.9 17.3 - - + -
151B VAL* 4.2 17.0 - - + -
180B MET* 3.0 45.0 + - + +
182B SER* 4.8 7.2 - - - +
199B CYS* 4.2 19.3 - - - -
201B ALA* 3.3 32.3 - - + -
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Residues in contact with ASN 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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140A THR* 4.8 6.4 - - - +
167A HIS* 3.7 10.1 - - + -
169A PHE* 3.5 18.8 - - - -
183A SER* 3.2 22.2 + - - -
185A THR* 5.5 1.7 + - - -
118B PRO* 3.2 3.3 - - - +
119B THR* 2.9 44.8 + - + +
140B PHE* 3.3 25.4 - - - +
141B LEU* 1.3 82.5 + - - +
143B ASN* 1.3 82.9 + - - +
144B PHE 3.5 1.8 - - - -
179B SER* 3.4 8.6 - - - +
180B MET 3.8 0.2 + - - -
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Residues in contact with ASN 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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167A HIS* 3.0 32.0 + - - -
116B ALA* 4.0 10.4 - - - +
117B ALA 3.9 9.9 - - - +
119B THR* 5.3 4.9 - - - +
142B ASN* 1.3 81.5 - - - +
144B PHE* 1.3 58.8 + - - +
172B ASP* 5.8 1.4 - - - -
175B ASP* 3.8 19.2 + - - +
177B THR* 3.1 32.5 + - + +
178B TYR 3.1 1.5 + - - -
179B SER* 2.9 9.1 + - - -
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Residues in contact with PHE 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ALA* 3.3 15.5 - - - +
118B PRO* 3.5 28.3 - - + -
141B LEU* 3.1 29.8 - - + -
143B ASN* 1.3 74.8 - - - +
145B TYR* 1.3 62.5 + - - +
146B PRO 3.2 20.6 - - - -
147B LYS* 3.5 28.0 - - - -
149B ILE* 3.6 31.0 - - + -
168B TRP* 4.8 4.0 - + - -
177B THR* 3.5 2.3 - - - -
178B TYR* 2.8 61.0 + - + +
179B SER* 3.5 13.5 - - - -
180B MET* 3.9 10.1 - - + -
203B HIS* 4.1 4.7 - - + -
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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