Contacts of the strand formed by residues 138 - 145 (chain A) in PDB entry 1K4R
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 VAL 138 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A ALA 3.9 0.5 - - - +
48A ILE* 3.3 5.9 - - - +
49A TYR* 2.7 75.1 + - + +
50A GLN* 5.5 0.4 - - - -
51A GLU 6.1 0.4 - - - +
136A LYS 3.8 10.5 - - - +
137A ILE* 1.3 77.5 - - - +
139A TYR* 1.3 64.8 + - - +
140A THR* 4.1 2.9 - - - +
164A SER* 3.9 25.4 - - - +
165A PHE 3.4 8.7 - - - +
166A THR* 4.0 13.9 - - + -
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Residues in contact with TYR 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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45A LEU* 3.9 10.1 - - + -
47A ALA 3.5 4.0 - - - -
48A ILE* 3.5 42.6 - - + +
137A ILE* 4.0 13.6 - - + +
138A VAL* 1.3 78.8 - - - +
140A THR* 1.3 59.8 + - - +
141A VAL* 5.4 0.7 - - + -
164A SER* 3.5 1.4 - - - -
165A PHE* 2.8 46.9 + - + +
188A VAL* 3.5 41.3 + - + -
191A GLY* 3.5 5.8 - - - -
192A VAL* 3.3 33.6 + - - +
194A LEU* 5.5 0.5 - - - +
287A HIS 3.7 16.4 - - - -
288A VAL* 3.7 24.9 - - + -
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Residues in contact with THR 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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45A LEU* 3.4 6.6 - - - +
46A ASP* 2.7 46.1 + - + +
47A ALA* 3.0 23.9 + - + -
49A TYR* 3.9 19.9 + - - -
138A VAL* 4.1 0.7 - - - +
139A TYR* 1.3 72.7 - - - +
141A VAL* 1.3 59.4 + - - +
142A LYS* 4.8 3.1 - - + +
162A THR* 3.4 30.5 - - + -
163A ALA 3.4 4.5 - - - +
164A SER* 3.5 14.5 + - - +
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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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25A LEU* 4.0 13.9 - - + -
43A VAL* 3.8 24.9 - - + -
44A TRP 3.4 10.3 - - - +
45A LEU* 4.2 14.6 - - + -
139A TYR* 4.8 1.6 - - + +
140A THR* 1.3 79.0 - - - +
142A LYS* 1.3 65.4 + - - +
143A VAL* 5.1 1.3 - - - +
162A THR* 3.5 2.9 - - - +
163A ALA* 2.8 39.0 + - - +
165A PHE* 3.8 28.5 - - + -
184A LEU* 4.1 17.9 - - + -
186A CYS* 4.1 10.8 - - - -
288A VAL* 4.9 2.9 - - + -
290A CYS* 4.4 1.1 - - - -
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Residues in contact with LYS 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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43A VAL* 3.3 6.2 - - - +
44A TRP* 2.9 69.0 + - + +
46A ASP* 3.2 36.8 - - + +
140A THR* 4.8 2.2 - - - +
141A VAL* 1.3 74.2 - - - +
143A VAL* 1.3 65.4 + - - +
160A ARG* 4.1 15.7 - - + +
161A LYS 3.3 4.9 - - - +
162A THR* 2.9 38.9 + - + +
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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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41A MET* 3.8 31.6 - - + -
42A ASP 3.3 8.7 - - - +
43A VAL* 4.3 20.0 - - + -
44A TRP* 4.6 0.2 - - - -
141A VAL* 4.7 0.7 - - + +
142A LYS* 1.3 79.9 - - - +
144A GLU* 1.3 64.3 + - - +
160A ARG* 3.3 4.1 - - - +
161A LYS 2.8 32.6 + - - +
174A LEU* 3.9 16.4 - - + -
176A MET* 3.8 13.8 - - + +
182A VAL* 4.7 7.2 - - + -
184A LEU* 3.9 30.1 - - + -
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Residues in contact with GLU 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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1A SER* 3.8 7.1 - - - -
2A ARG* 2.9 31.6 + - - +
41A MET* 3.6 4.0 - - - -
42A ASP* 2.8 39.9 + - + +
44A TRP* 4.0 13.0 - - + -
143A VAL* 1.3 76.2 - - - +
145A PRO* 1.3 77.9 - - + +
146A HIS* 4.4 0.7 - - - -
151A VAL* 6.0 0.2 - - - +
157A HIS* 3.5 31.7 - - + +
160A ARG* 2.7 45.2 + - + +
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Residues in contact with PRO 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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1A SER* 6.1 0.3 - - - -
39A PRO* 5.9 0.9 - - + -
40A SER 3.8 0.7 - - - +
41A MET* 3.6 22.0 - - + -
144A GLU* 1.3 93.6 - - + +
146A HIS* 1.3 60.7 + - - +
147A THR* 3.3 24.0 + - + +
157A HIS* 3.7 12.8 + - + -
159A GLY* 3.2 29.2 - - - +
176A MET* 3.6 13.5 - - + +
179A TYR* 4.0 31.0 - - + -
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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