Contacts of the strand formed by residues 117 - 122 (chain G) in PDB entry 1P8Z
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 117 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166A TYR* 5.7 5.2 - - - +
167A GLU* 3.6 5.8 - - - +
83G TYR 3.2 9.0 + - - +
84G ASP* 3.4 13.4 - - - +
85G LEU 3.0 23.1 + - - +
115G ARG 4.8 4.3 - - - +
116G ALA* 1.3 75.3 - - - +
118G GLN* 1.3 63.9 + - - +
119G HIS* 3.4 32.4 - - + +
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Residues in contact with GLN 118 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A THR* 2.9 48.2 + - - +
149A THR* 5.9 0.2 - - - +
167A GLU* 2.9 46.2 + - + +
85G LEU* 3.3 7.6 - - + -
87G TYR* 5.1 1.6 - - + -
105G THR* 3.5 24.5 - - + +
106G VAL* 3.8 8.0 - - - +
109G ASP* 2.5 37.2 - - + +
117G VAL* 1.3 76.6 - - - +
119G HIS* 1.3 70.2 + - - +
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Residues in contact with HIS 119 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84G ASP* 2.8 22.3 + - - -
85G LEU 2.7 10.0 + - - +
86G HIS* 3.2 32.6 + + - +
87G TYR* 3.0 33.6 + - - -
117G VAL* 3.4 32.8 - - + +
118G GLN* 1.3 74.6 + - - +
120G ARG* 1.3 60.1 + - - +
121G GLU* 3.4 19.1 + - - +
127G SER* 5.7 0.9 - - - -
129G THR* 6.0 3.4 - - + +
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Residues in contact with ARG 120 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A SER 4.1 3.6 + - - -
146A GLY 2.7 25.7 + - - -
147A ARG* 3.4 46.9 - - - +
296A ASN* 4.9 3.6 + - - -
87G TYR* 3.5 32.6 - - + +
89G LEU* 3.4 24.5 - - + +
119G HIS* 1.3 70.9 - - - +
121G GLU* 1.3 63.7 + - - +
122G VAL* 3.3 27.7 + - + +
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Residues in contact with GLU 121 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86G HIS* 2.6 47.5 + - + -
87G TYR 2.9 14.2 + - - +
88G TRP* 3.2 18.8 - - + -
89G LEU* 2.8 28.1 + - - +
119G HIS* 3.4 10.4 - - - +
120G ARG* 1.3 77.3 - - - +
122G VAL* 1.3 63.5 + - - +
123G GLN 4.2 0.2 + - - -
125G PHE 5.6 0.2 - - - -
126G GLU* 3.5 5.9 - - + +
127G SER* 2.9 41.8 + - - -
130G PHE* 3.5 19.0 - - + +
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Residues in contact with VAL 122 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88G TRP* 4.7 0.2 - - - -
89G LEU* 4.0 12.8 - - + +
91G ASN* 4.9 7.9 - - - +
120G ARG* 3.3 42.0 + - + +
121G GLU* 1.3 77.5 - - - +
123G GLN* 1.3 75.5 + - - +
124G GLY 3.3 0.2 + - - -
125G PHE* 2.8 34.1 + - + -
126G GLU* 3.5 10.7 + - - +
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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