Contacts of the strand formed by residues 140 - 149 (chain A) in PDB entry 4Z1K
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 140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A TYR* 3.6 7.5 - - - -
121A VAL* 4.2 12.3 - - + -
122A HIS 3.2 7.4 - - - +
123A TRP* 3.6 22.2 - - + -
130A PHE* 3.6 30.7 - - + -
133A ALA* 4.2 2.9 - - + -
134A VAL* 4.1 10.1 - - + -
138A ASP 4.6 0.5 - - - -
139A GLY* 1.3 87.2 + - - +
141A ALA* 1.3 63.0 + - - +
142A VAL* 4.8 2.9 - - + -
197A LEU* 3.7 30.3 - - + -
205A CYS* 2.9 24.7 + - - +
206A VAL* 3.5 9.6 - - + -
207A THR* 2.9 27.0 + - - -
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Residues in contact with ALA 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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79A LEU* 4.0 10.8 - - + -
84A LEU* 3.8 31.2 - - + -
88A TYR* 3.5 21.7 - - + -
122A HIS* 2.9 40.1 + - - -
140A LEU* 1.3 73.7 - - - +
142A VAL* 1.3 62.1 + - - +
207A THR 3.3 7.9 - - - +
209A ILE* 4.7 1.8 - - + -
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Residues in contact with VAL 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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79A LEU* 5.4 0.4 - - - -
119A HIS* 3.7 23.8 - - + -
120A LEU 3.4 10.5 - - - +
121A VAL* 4.3 18.2 - - + -
140A LEU* 4.8 4.9 - - + -
141A ALA* 1.3 77.5 - - - +
143A LEU* 1.3 61.7 + - - +
206A VAL* 3.7 22.9 - - + -
207A THR 3.2 7.1 + - - +
208A TRP* 3.4 38.7 - - + -
209A ILE* 3.0 27.9 + - - +
302A 4KB 3.8 14.1 - - + +
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Residues in contact with LEU 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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47A LEU* 3.8 8.1 - - + -
49A VAL* 4.4 20.6 - - + -
51A TYR* 4.2 11.2 - - - +
79A LEU* 4.6 9.4 - - + +
118A LEU 3.4 3.8 - - - +
119A HIS* 3.5 0.5 - - - -
120A LEU* 2.9 59.0 + - + +
122A HIS* 4.1 9.6 + - + -
141A ALA 4.1 1.0 - - - -
142A VAL* 1.3 70.8 - - - +
144A GLY* 1.3 59.4 + - - +
145A ILE* 4.1 6.7 + - + -
184A LEU* 4.5 11.4 - - + -
188A LEU* 5.8 0.4 - - + -
209A ILE* 3.3 31.9 - - + +
211A LEU* 3.8 26.0 - - + -
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Residues in contact with GLY 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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117A GLU* 4.5 6.5 - - - -
118A LEU 3.2 7.2 - - - -
119A HIS* 4.0 12.3 - - - -
142A VAL 3.7 2.4 + - - -
143A LEU* 1.3 71.8 - - - +
145A ILE* 1.3 66.8 + - - +
208A TRP* 4.6 4.9 - - - -
209A ILE 2.8 13.7 + - - +
210A VAL* 3.5 11.6 - - - +
211A LEU* 2.9 28.6 + - - +
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Residues in contact with ILE 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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117A GLU* 3.4 3.7 - - - +
118A LEU* 2.8 41.1 + - + +
120A LEU* 3.8 18.8 - - + -
143A LEU* 4.4 5.6 - - + -
144A GLY* 1.3 81.2 - - - +
146A PHE* 1.3 74.3 + - - +
147A LEU* 3.4 2.4 - - - +
183A LEU 4.0 9.9 - - - +
184A LEU* 3.6 31.2 - - + -
185A PRO* 4.1 7.4 - - + -
211A LEU* 3.8 22.9 - - + +
213A GLU 4.4 7.2 - - - +
215A ILE* 4.0 27.8 - - + -
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Residues in contact with PHE 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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33A ILE* 4.7 0.9 - - + -
105A SER* 4.0 9.9 - - - -
107A HIS* 3.4 34.1 - - + -
109A VAL* 3.5 30.7 - - + -
114A TYR* 3.4 42.0 - + + -
116A ALA 3.8 1.8 - - - -
117A GLU* 3.6 17.7 - - + -
145A ILE* 1.3 75.8 - - - +
147A LEU* 1.3 56.0 + - - +
191A TRP* 4.5 2.9 - + - -
210A VAL* 3.5 29.6 - - + -
211A LEU 3.8 16.2 + - - -
212A LYS 4.9 6.1 - - - -
213A GLU 5.1 0.2 + - - -
214A PRO* 3.2 10.0 - - + +
215A ILE* 2.9 34.1 + - - +
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Residues in contact with LEU 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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95A PHE* 3.8 22.0 - - + -
114A TYR* 3.4 5.7 - - - +
115A ALA* 3.1 27.5 + - + +
116A ALA* 2.9 33.6 + - + +
117A GLU* 4.3 0.4 - - - -
118A LEU* 3.8 23.1 - - + +
145A ILE 3.4 17.5 - - - +
146A PHE* 1.3 75.3 - - - +
148A LYS* 1.3 59.6 + - - +
156A LEU* 4.8 2.0 - - + -
215A ILE* 3.4 26.2 - - + +
217A VAL* 3.7 31.9 - - + -
222A VAL* 6.2 0.7 - - + -
225A PHE* 4.5 8.1 - - + -
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Residues in contact with LYS 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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112A LYS* 6.2 0.7 - - - -
114A TYR* 4.2 16.4 - - + -
115A ALA* 4.6 3.1 - - - +
146A PHE 4.2 0.2 - - - -
147A LEU* 1.3 75.0 - - - +
149A VAL* 1.3 66.3 + - - +
150A GLY* 6.3 0.7 - - - -
214A PRO* 3.8 35.4 + - + +
215A ILE 3.0 9.4 + - - +
216A SER* 2.7 33.7 + - - +
217A VAL* 2.9 28.5 + - - +
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Residues in contact with VAL 149 (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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101A ASP* 3.7 39.0 - - + +
115A ALA* 3.9 18.3 - - + +
148A LYS* 1.3 79.1 - - - +
150A GLY* 1.3 62.1 + - - +
217A VAL* 3.3 9.6 - - + +
219A SER* 3.6 32.8 - - - +
222A VAL* 4.0 15.9 - - + -
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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