Contacts of the strand formed by residues 143 - 151 (chain A) in PDB entry 3UP1
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 LEU 143 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A PRO* 3.7 24.7 - - + -
132A THR* 3.8 5.2 - - + +
134A HIS* 3.5 38.8 - - + +
140A VAL* 3.9 15.5 - - + +
141A LYS 3.9 4.3 + - - +
142A VAL* 1.3 80.0 - - - +
144A MET* 1.3 59.9 + - - +
145A HIS* 3.8 31.9 - - + +
164A SER* 3.8 26.2 + - - +
187A SER* 3.8 10.8 - - - -
188A ILE 3.2 19.1 - - - +
189A PRO* 3.9 7.0 - - + -
190A ASP* 3.8 7.0 - - - +
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Residues in contact with MET 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A LEU* 1.3 73.0 - - - +
145A HIS* 1.3 70.7 + - - +
162A ASN* 4.0 28.7 - - + +
163A LEU 3.8 9.0 - - - +
164A SER* 4.8 2.5 - - - +
187A SER* 3.2 3.1 - - - -
188A ILE* 2.8 48.3 + - + -
190A ASP* 3.6 23.8 - - + +
197A TRP* 3.5 35.8 - - + -
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Residues in contact with HIS 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A PRO* 4.5 0.8 - - + +
130A PHE* 3.6 28.7 - + + -
132A THR* 4.3 13.8 - - + +
143A LEU* 3.8 23.5 - - + +
144A MET* 1.3 75.7 - - - +
146A ASP* 1.3 59.4 + - - +
147A VAL 4.0 0.4 - - - -
162A ASN* 3.2 8.3 - - - +
163A LEU* 2.7 50.3 + - + +
164A SER* 3.7 16.3 + - - -
165A SER 3.3 24.0 - - - -
166A THR* 4.3 8.1 - - - +
185A VAL* 4.1 3.4 - - + -
186A ARG 3.2 4.8 + - - +
187A SER* 2.8 34.2 + - - -
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Residues in contact with ASP 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A HIS* 1.3 73.7 - - - +
147A VAL* 1.3 62.8 + - - +
160A HIS* 2.7 44.4 + - - +
161A VAL 3.6 2.8 - - - +
162A ASN* 3.8 10.7 - - - +
185A VAL* 3.4 3.2 - - - -
186A ARG* 2.7 62.0 + - + +
197A TRP* 3.5 27.5 - - + -
200A TRP* 3.6 5.5 - - - -
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Residues in contact with VAL 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A VAL* 4.8 2.7 - - + -
130A PHE* 4.0 9.2 - - + -
146A ASP* 1.3 71.9 - - - +
148A ALA* 1.3 60.9 + - - +
149A TYR* 4.6 5.2 - - + -
159A THR 3.6 1.2 - - - +
160A HIS* 3.2 4.2 - - - -
161A VAL* 2.8 42.9 + - + +
163A LEU* 3.6 24.9 - - + -
168A LEU* 3.9 23.8 - - + -
183A ILE* 3.7 32.5 - - + -
184A LYS 3.5 4.9 - - - +
185A VAL* 3.8 26.0 - - + -
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Residues in contact with ALA 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A ASP 3.9 0.6 + - - -
147A VAL* 1.3 74.4 - - - +
149A TYR* 1.3 61.4 + - - +
158A TRP* 3.5 21.4 - - + -
159A THR 3.3 5.4 - - - +
160A HIS* 3.6 29.8 - - + +
183A ILE* 3.2 3.7 - - - +
184A LYS* 2.8 37.2 + - + +
200A TRP* 3.9 17.0 - - + -
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Residues in contact with TYR 149 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A VAL* 4.6 6.7 - - + -
148A ALA* 1.3 78.6 - - - +
150A ARG* 1.3 62.1 + - - +
158A TRP* 3.5 3.1 - - - -
159A THR* 2.9 72.4 + - + +
161A VAL* 4.2 11.9 - - + +
170A LEU* 3.5 40.7 - - + +
174A LYS* 5.6 4.7 + - - +
175A LEU* 3.7 24.4 - - + +
181A TYR* 4.1 19.5 - + + -
182A GLU 3.0 13.5 - - - +
183A ILE* 3.6 19.7 - - + -
206A PHE* 5.5 1.3 - + + -
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Residues in contact with ARG 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A TYR* 1.3 75.7 - - - +
151A GLN* 1.3 66.0 + - - +
152A GLU 4.8 6.8 + - - -
154A ASP* 2.5 40.3 + - + -
155A GLU* 4.0 11.7 - - - +
157A LYS* 3.3 27.2 - - - +
158A TRP* 3.2 46.3 - - + +
181A TYR* 3.4 10.8 - - - -
182A GLU* 2.7 61.8 + - + +
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Residues in contact with GLN 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A ARG* 1.3 82.2 - - - +
152A GLU* 1.3 66.9 + - - +
153A LYS* 3.1 12.1 + - - +
154A ASP* 3.3 33.9 + - + +
176A GLN* 3.2 29.8 - - - +
179A ALA* 4.0 18.0 - - - +
180A MET 3.4 7.6 + - - +
181A TYR* 3.5 27.5 + - + +
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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
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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