Contacts of the strand formed by residues 134 - 140 (chain A) in PDB entry 4YET
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 ALA 134 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A ILE* 5.0 3.6 - - + -
96A LYS* 4.1 36.5 + - + +
97A ILE* 4.2 7.4 - - + -
100A LYS* 3.3 31.6 - - + +
101A PHE* 4.7 1.6 - - + -
126A LEU* 4.2 16.4 - - + -
127A VAL 3.3 10.5 - - - +
128A LEU* 4.7 1.8 - - - +
132A GLY 4.3 0.4 + - - -
133A THR* 1.3 78.1 + - - +
135A ASP* 1.3 64.6 + - - +
154A LEU* 5.2 1.1 - - + -
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Residues in contact with ASP 135 (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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100A LYS* 3.9 18.5 + - - -
101A PHE* 4.4 7.2 - - - -
126A LEU* 3.5 7.4 - - - +
127A VAL* 2.8 36.9 + - + +
129A LYS* 3.3 41.3 + - + +
134A ALA* 1.3 77.1 - - - +
136A ILE* 1.3 90.6 + - - +
137A VAL* 5.2 4.6 - - + +
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Residues in contact with ILE 136 (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 PHE* 4.0 12.6 - - + -
107A PHE* 3.6 25.6 - - + -
110A ASP* 3.7 40.4 - - + +
111A PHE* 3.4 27.6 - - + +
114A LEU* 4.0 17.4 - - + +
125A TRP 3.2 8.7 - - - +
126A LEU* 4.2 3.6 - - + -
135A ASP* 1.3 98.8 + - - +
137A VAL* 1.3 68.9 + - - +
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Residues in contact with VAL 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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114A LEU* 3.8 9.5 - - - +
124A GLY* 3.6 2.9 - - - -
125A TRP* 2.9 52.2 + - + -
127A VAL* 3.8 22.2 - - + -
129A LYS* 6.2 1.8 - - + -
135A ASP* 5.2 5.6 - - - +
136A ILE* 1.3 81.6 - - - +
138A GLN* 1.3 62.6 + - - +
145A PRO* 5.2 0.7 - - + -
150A LEU* 4.0 44.4 - - + +
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Residues in contact with GLN 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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114A LEU* 4.0 28.0 - - + +
117A GLY 5.2 0.7 - - - -
118A HIS* 2.8 44.3 + - + +
123A TRP 3.3 13.0 - - - +
125A TRP* 4.3 0.7 - - - -
137A VAL* 1.3 77.0 - - - +
139A THR* 1.3 69.3 + - - +
148A GLU* 4.7 1.9 - - - +
150A LEU* 4.0 9.0 - - - +
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Residues in contact with THR 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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118A HIS* 3.3 9.5 - - - -
122A GLY* 3.3 2.3 - - - -
123A TRP* 2.9 36.3 + - - +
125A TRP* 2.9 27.2 + - + +
138A GLN* 1.3 79.5 - - - +
140A HIS* 1.3 61.7 + - - +
143A GLY* 2.8 37.7 + - - +
145A PRO 4.0 8.7 - - - -
148A GLU* 4.0 10.3 - - - +
150A LEU* 3.8 22.0 - - + -
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Residues in contact with HIS 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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118A HIS* 2.8 24.6 + + + +
119A PHE 3.1 25.1 - - - -
121A SER 3.0 16.0 + - - -
139A THR* 1.3 75.0 - - - +
141A ASP* 1.3 83.6 + - - +
142A ALA 3.1 0.7 + - - -
143A GLY* 2.8 27.2 + - - -
148A GLU* 5.1 1.8 + - - -
140B HIS* 3.9 3.1 + + - -
141B ASP* 2.6 35.3 + - - -
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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