Contacts of the strand formed by residues 139 - 145 (chain B) in PDB entry 1A4K
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 139 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B LEU* 3.0 35.5 + - - +
138B LEU* 1.3 81.6 - - - +
140B CYS* 1.3 60.3 + - - -
154B TRP* 3.8 5.6 - - - -
180B SER 3.4 12.1 - - - -
181B VAL* 3.9 6.5 - - - -
211B VAL* 3.2 18.6 - - - +
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Residues in contact with CYS 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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121B VAL* 4.3 9.0 - - + -
122B PHE 3.7 6.7 - - - -
123B PRO* 4.8 0.4 - - - -
124B LEU* 3.4 10.0 - - - +
139B GLY* 1.3 79.1 - - - -
141B LEU* 1.3 59.1 + - - +
142B VAL* 4.0 4.4 + - + +
152B VAL* 5.5 1.1 - - + -
154B TRP* 3.8 4.7 - - + -
179B SER* 3.4 4.5 - - - -
180B SER* 2.9 35.1 + - - +
196B CYS* 2.0 53.2 - - + -
198B VAL* 5.6 0.9 - - + -
209B LYS* 4.4 4.3 - - - -
211B VAL* 3.6 16.8 - - - -
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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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124A GLN* 4.5 2.9 - - - +
131A SER* 3.7 31.0 - - - +
133A VAL* 4.6 15.7 - - + -
178A THR* 4.8 9.2 - - + +
120B SER 3.6 2.1 - - - +
121B VAL* 3.6 2.6 - - - -
122B PHE* 2.7 57.5 + - + +
123B PRO 5.0 0.4 - - - +
124B LEU* 3.7 15.6 - - + +
140B CYS* 1.3 73.2 - - - +
142B VAL* 1.3 59.6 + - - +
143B LYS* 3.9 18.3 + - + -
177B SER* 4.2 14.8 - - - +
178B LEU 3.8 17.0 - - - +
179B SER* 4.5 8.5 - - - +
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Residues in contact with VAL 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B PRO* 3.5 27.1 - - + -
120B SER 3.7 4.3 - - - +
121B VAL* 4.5 4.3 - - + +
140B CYS* 4.9 5.4 - - + +
141B LEU* 1.3 73.9 - - - +
143B LYS* 1.3 58.7 + - - +
145B TYR* 3.8 12.3 - - + -
150B VAL* 4.1 4.0 - - + -
152B VAL* 4.3 13.9 - - + -
177B SER* 3.7 1.2 - - - -
178B LEU* 2.9 66.6 + - + +
179B SER 5.3 0.2 - - - -
180B SER* 5.4 1.1 - - - +
198B VAL* 3.8 27.8 - - + -
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Residues in contact with LYS 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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124A GLN* 4.0 21.1 - - - +
129A THR* 4.1 5.4 - - - +
131A SER* 3.4 21.5 + - - +
180A THR* 4.1 12.5 + - - +
119B PRO* 3.4 2.1 - - - +
120B SER* 3.0 30.3 + - - -
122B PHE* 3.9 23.8 - - + -
141B LEU* 4.2 12.3 - - + -
142B VAL* 1.3 74.0 - - - +
144B ASP* 1.3 97.4 + - - +
145B TYR* 3.6 2.0 - - - -
171B GLN* 3.4 19.2 - - - +
176B TYR 3.9 2.2 - - - -
177B SER* 3.0 23.8 - - - +
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Residues in contact with ASP 144 (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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117B LYS* 2.9 38.0 + - - +
118B GLY 3.0 6.2 - - - +
120B SER* 5.1 4.1 + - - +
122B PHE* 5.6 1.6 - - - -
143B LYS* 1.3 100.9 - - - +
145B TYR* 1.3 58.2 + - - +
171B GLN* 2.8 27.9 - - - +
173B SER* 4.5 2.9 + - - -
175B LEU* 3.6 23.6 - - + +
176B TYR 2.9 11.5 + - - -
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Residues in contact with TYR 145 (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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117B LYS* 3.1 13.9 - - - +
119B PRO* 3.4 34.3 - - + -
142B VAL* 3.8 25.6 - - + -
143B LYS 4.4 0.7 - - - -
144B ASP* 1.3 75.5 - - - +
146B PHE* 1.3 68.5 + - - +
147B PRO 3.9 1.8 - - - -
148B GLU* 3.9 22.2 + - - -
150B VAL* 4.0 19.6 + - + +
168B ALA* 2.9 30.8 - - - +
175B LEU* 3.8 3.4 - - - +
176B TYR* 2.9 57.4 + - + +
177B SER* 4.0 1.8 - - - -
178B LEU* 3.4 12.6 - - + +
200B HIS* 3.7 17.0 - + - +
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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