Contacts of the strand formed by residues 125 - 130 (chain E) in PDB entry 3QS7
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 125 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92E GLN* 5.7 4.7 - - + -
93E VAL 3.4 7.0 - - - +
94E LEU* 3.8 18.8 - - + -
116E PRO* 3.3 1.9 - - - +
117E HIS* 2.9 44.9 + - + +
118E PHE* 4.6 1.7 - - - +
124E GLY* 1.4 71.8 - - - -
126E VAL* 1.3 60.1 + - - +
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Residues in contact with VAL 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92E GLN* 3.2 4.7 - - - +
93E VAL* 3.0 35.4 + - + +
103E CYS* 4.7 9.2 - - + -
114E CYS* 6.2 0.7 - - + -
116E PRO* 3.6 20.6 - - + -
124E GLY 4.3 0.6 + - - -
125E VAL* 1.3 73.9 - - - +
127E SER* 1.4 62.0 + - - +
143E LEU* 3.8 27.6 - - + -
145E ILE* 4.9 7.6 - - + -
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Residues in contact with SER 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90E THR* 5.9 3.8 - - - -
91E LEU 3.3 8.1 - - - -
92E GLN* 3.7 18.6 - - - -
114E CYS* 5.6 6.2 - - - +
116E PRO* 4.8 3.8 - - - +
126E VAL* 1.4 78.1 - - - +
128E MET* 1.3 62.4 + - - +
129E VAL* 4.2 2.7 - - - -
143E LEU* 5.3 3.1 - - - +
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Residues in contact with MET 128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91E LEU* 2.9 45.2 + - + +
105E TRP* 6.1 5.4 - - + -
127E SER* 1.3 72.3 - - - +
129E VAL* 1.3 59.0 + - - +
130E ILE* 5.6 1.1 - - - -
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Residues in contact with VAL 129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E ILE 4.3 0.9 - - - +
90E THR* 3.8 27.6 - - - +
127E SER* 4.2 2.8 - - - -
128E MET* 1.3 74.0 - - - +
130E ILE* 1.3 67.9 + - - +
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Residues in contact with ILE 130 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83E VAL* 5.7 4.5 - - + -
87E ALA* 4.0 5.2 - - + +
88E SER* 3.2 3.3 - - - -
89E ILE* 2.9 61.3 + - + +
91E LEU* 3.8 18.4 - - + -
128E MET 5.5 1.3 - - - +
129E VAL* 1.3 80.3 - - - +
131E LEU* 1.4 60.9 + - - +
132E LYS 5.6 0.2 - - - -
133E MET* 3.8 28.9 - - + -
137E GLN* 5.2 15.0 - - + +
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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