Contacts of the strand formed by residues 137 - 143 (chain A) in PDB entry 3ESF
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 137 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A LEU* 4.2 8.7 - - + -
98A ALA* 3.8 37.7 - - + +
99A ILE* 3.8 21.3 - - + +
102A SER* 2.8 25.1 + - - +
103A PHE* 3.6 16.7 - - + -
128A LEU* 3.8 15.0 - - + -
129A VAL 3.3 5.4 - - - +
130A GLN* 3.6 31.6 - - + +
135A LYS 3.7 2.3 + - - +
136A LYS* 1.3 76.9 - - - +
138A LYS* 1.3 62.1 + - - +
157A ILE* 4.4 7.2 - - + -
195A PHE* 3.9 17.0 - - + -
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Residues in contact with LYS 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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103A PHE* 3.7 11.9 - - - -
112A GLU* 5.9 0.2 - - - +
128A LEU* 3.6 3.6 - - - +
129A VAL* 2.9 48.4 + - + +
131A ASP* 5.5 7.6 + - + +
136A LYS* 5.2 4.0 - - + +
137A LEU* 1.3 76.4 - - - +
139A VAL* 1.3 70.1 + - - +
140A PHE* 4.1 21.9 - - + -
154A LEU* 3.7 29.7 - - - +
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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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103A PHE* 3.9 14.5 - - + -
109A PHE* 4.1 16.2 - - + -
112A GLU* 3.7 38.7 + - + +
113A PHE* 4.0 24.7 - - + +
116A ALA* 3.7 30.5 - - + -
127A TRP 3.3 12.3 - - - +
138A LYS* 1.3 82.3 - - - +
140A PHE* 1.3 65.5 + - - +
141A GLN* 5.4 0.4 - - + -
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Residues in contact with PHE 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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126A ALA* 3.9 0.2 - - - -
127A TRP* 2.8 46.8 + + + +
129A VAL* 3.9 22.7 - - + -
138A LYS* 4.1 18.8 - - + -
139A VAL* 1.3 77.5 - - - +
141A GLN* 1.3 70.7 + - - +
142A THR* 3.5 27.8 - - + -
148A PRO* 4.0 16.2 - - + -
151A GLU* 3.9 23.1 - - + -
154A LEU* 3.7 32.3 - - + -
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Residues in contact with GLN 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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116A ALA* 3.6 45.8 - - + +
119A GLY 5.1 0.5 - - - -
120A HIS* 2.9 38.2 + - + +
125A TRP 3.4 9.6 - - - +
126A ALA* 4.8 2.5 - - + -
140A PHE* 1.3 91.4 - - - +
142A THR* 1.3 68.6 + - - +
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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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120A HIS* 3.3 8.0 - - - -
124A GLY* 3.2 2.3 - - - -
125A TRP* 2.9 40.7 + - - +
127A TRP* 3.0 21.3 + - - +
140A PHE* 3.5 23.6 - - + -
141A GLN* 1.3 80.0 - - - +
143A HIS* 1.3 60.0 + - - +
146A GLY* 2.8 40.1 + - - +
147A CYS 3.9 3.8 - - - +
148A PRO 4.2 3.6 - - - -
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Residues in contact with HIS 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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120A HIS* 2.8 17.6 + + + +
121A PHE 3.0 24.2 - - - -
123A SER 2.8 24.1 + - - -
142A THR* 1.3 73.9 - - - +
144A ASP* 1.3 86.5 + - - +
145A ALA 3.1 0.9 + - - -
146A GLY* 2.9 21.9 + - - -
143B HIS* 3.7 4.0 + + - -
144B ASP* 2.6 37.5 + - - -
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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