Contacts of the strand formed by residues 136 - 143 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A LYS* 3.6 4.2 + - - +
48A THR* 3.4 4.5 - - - -
49A THR* 2.8 50.0 + - + +
51A LYS* 4.2 30.9 + - + +
135A LEU* 1.3 70.1 - - - +
137A TYR* 1.3 63.8 + - - +
138A THR* 3.8 5.0 + - - +
163A MET* 3.4 49.4 - - + +
164A ILE 3.6 1.6 - - - -
165A THR* 3.9 17.0 + - + +
54H ARG* 6.2 0.2 - - - +
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Residues in contact with TYR 137 (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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45A LEU* 3.9 20.2 - - + -
47A LYS 3.7 3.4 - - - -
48A THR* 3.5 32.9 - - + +
132A ILE* 5.4 0.9 - - - +
135A LEU* 3.8 34.9 - - + +
136A GLU* 1.3 73.0 - - - +
138A THR* 1.3 61.0 + - - +
139A VAL 3.9 0.8 + - - -
162A ALA 3.3 4.9 - - - +
163A MET* 3.4 1.6 - - - -
164A ILE* 2.7 60.2 + - + +
165A THR 5.0 0.2 - - - -
166A PRO* 4.9 0.9 - - + -
187A PRO* 3.5 35.9 - - + +
188A ARG 5.0 1.7 + - - -
189A SER* 5.1 9.7 - - - -
279A PHE* 6.0 1.0 - - + +
281A GLY 6.3 2.0 - - - -
282A HIS 5.5 3.1 + - - -
283A LEU* 3.7 28.5 - - + -
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Residues in contact with THR 138 (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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45A LEU* 3.6 6.0 - - - +
46A THR* 2.9 34.8 + - + -
47A LYS* 2.8 49.4 + - + +
136A GLU* 4.2 5.9 + - - +
137A TYR* 1.3 70.9 - - - +
139A VAL* 1.3 62.3 + - - +
140A VAL* 5.1 0.7 - - + -
161A THR* 4.3 24.2 - - + +
162A ALA 3.4 8.5 - - - +
163A MET* 4.6 16.5 - - + +
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Residues in contact with VAL 139 (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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25A LEU* 3.9 23.3 - - + -
43A PHE* 4.2 20.9 - - + -
44A GLU 3.5 11.9 - - - +
45A LEU* 3.9 19.3 - - + -
137A TYR 4.6 1.1 - - - +
138A THR* 1.3 76.5 - - - +
140A VAL* 1.3 64.5 + - - +
141A VAL* 4.1 1.0 + - + +
160A VAL 3.7 1.7 - - - +
161A THR* 3.5 1.4 - - - -
162A ALA* 2.8 41.0 + - + +
164A ILE* 3.9 19.7 - - + -
183A LEU* 4.3 15.7 - - + -
185A CYS* 5.4 0.2 - - - -
283A LEU* 3.9 13.2 - - + -
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Residues in contact with VAL 140 (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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2A ARG* 3.6 41.3 - - - +
42A ASP 3.1 13.2 - - - +
43A PHE* 3.5 1.6 - - - -
44A GLU* 2.9 27.7 + - + +
46A THR* 3.3 28.5 - - + +
138A THR* 5.1 2.7 - - + -
139A VAL* 1.3 77.0 - - - +
141A VAL* 1.3 59.4 + - - +
142A THR* 3.7 7.9 - - - +
158A HIS 5.2 0.4 - - - +
159A GLY 4.4 3.6 - - - +
160A VAL 3.5 14.8 - - - +
161A THR* 3.8 23.8 - - + -
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Residues in contact with VAL 141 (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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41A LEU* 3.9 26.7 - - + -
42A ASP 3.4 2.9 - - - +
43A PHE* 3.7 35.9 - - + -
139A VAL* 4.1 2.0 + - + +
140A VAL* 1.3 71.6 - - - +
142A THR* 1.3 62.7 + - - +
159A GLY* 3.5 1.0 - - - -
160A VAL* 2.9 43.5 + - + +
162A ALA* 5.9 1.1 - - + -
173A VAL* 3.9 23.3 - - + -
175A LEU* 3.9 29.3 - - + +
181A LEU* 4.4 2.9 - - + -
183A LEU* 6.5 0.4 - - + -
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Residues in contact with THR 142 (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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1A MET* 4.5 4.9 - - + +
2A ARG* 3.2 46.1 + - + +
41A LEU* 3.5 4.7 - - - -
42A ASP* 2.7 42.1 + - - +
140A VAL* 3.7 7.8 - - - +
141A VAL* 1.3 74.8 + - - +
143A VAL* 1.3 72.4 + - - +
145A ASN* 5.4 0.7 - - - +
158A HIS* 4.5 18.4 - - + -
159A GLY* 3.8 18.4 - - - +
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Residues in contact with VAL 143 (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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1A MET 3.4 12.4 + - - -
39A PRO* 4.3 5.6 - - + -
40A THR 3.7 13.2 - - - +
41A LEU* 3.8 17.4 - - + +
141A VAL 4.3 0.6 + - - -
142A THR* 1.3 79.7 - - - +
144A HIS* 1.3 63.9 + - - +
145A ASN* 3.0 32.8 - - - +
175A LEU* 5.4 6.7 - - + +
178A TYR* 3.6 56.8 - - + +
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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