Contacts of the strand formed by residues 129 - 133 (chain v) in PDB entry 6FF7
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 129 (chain v).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123v VAL* 3.7 2.1 - - - +
124v ASP* 3.1 28.9 + - + +
127v GLY* 3.9 1.1 - - - -
128v ARG* 1.3 81.1 + - + +
130v VAL* 1.3 64.1 + - - +
141v VAL* 5.8 4.7 - - + -
142v TYR 3.2 13.0 - - - +
143v ILE* 4.7 2.9 - - + -
144v LEU* 4.3 3.3 - - - +
180v PRO* 4.8 17.5 - - + -
213v LEU* 5.3 10.5 - - + -
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Residues in contact with VAL 130 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122v ALA 3.6 11.0 - - - +
123v VAL* 4.3 9.0 - - + +
129v ALA* 1.3 76.6 - - - +
131v MET* 1.3 60.7 + - - +
132v ILE 4.1 0.6 + - - -
140v LEU 3.7 1.0 - - - +
141v VAL* 3.4 3.9 - - - -
142v TYR* 2.9 39.7 + - + +
144v LEU* 6.3 1.6 - - + -
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Residues in contact with MET 131 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121v LEU* 3.5 2.8 - - - +
122v ALA* 2.9 50.5 + - + +
130v VAL* 1.3 73.2 - - - +
132v ILE* 1.3 62.8 + - - +
133v SER* 5.3 2.9 - - - -
139v LYS* 5.8 4.9 - - + -
140v LEU 3.3 10.3 - - - +
141v VAL* 4.4 6.1 - - + +
182v PHE* 4.9 14.1 - - + -
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Residues in contact with ILE 132 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81v GLY* 6.4 2.7 - - - -
117v PRO* 3.9 16.2 - - + +
118v GLY* 4.9 6.5 - - - +
120v PHE 3.8 6.1 - - - +
121v LEU* 4.7 3.6 - - + +
130v VAL 4.1 1.0 + - - -
131v MET* 1.3 73.0 - - - +
133v SER* 1.3 59.7 + - - +
139v LYS* 3.5 2.6 - - - +
140v LEU* 2.9 37.4 + - + +
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Residues in contact with SER 133 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117v PRO* 3.8 7.3 - - - +
118v GLY 4.4 0.2 - - - +
119v GLN 3.3 6.6 + - - -
120v PHE* 2.9 42.7 + - - +
131v MET* 5.3 3.6 - - - -
132v ILE* 1.3 76.2 - - - +
134v ALA* 1.3 65.4 + - - +
138v GLN 4.2 4.5 - - - -
139v LYS* 4.3 14.1 - - - -
167v VAL* 5.3 5.8 - - - -
170v VAL* 4.6 17.9 - - - -
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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