Contacts of the strand formed by residues 131 - 135 (chain G) in PDB entry 4NQD
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 131 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120G GLN* 3.6 5.7 - - - +
121G LEU* 2.8 48.4 + - + +
130G SER* 1.4 72.6 - - - +
132G CYS* 1.4 67.5 + - - +
133G LEU 4.6 0.7 - - - +
172G VAL* 3.8 18.4 - - + -
173G ALA 3.6 2.7 - - - -
174G TRP* 3.7 12.8 - - + -
129H PHE* 4.1 20.8 - - + -
145H VAL* 3.8 18.4 - - + -
147H LEU* 3.7 40.2 - - + -
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Residues in contact with CYS 132 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118G VAL* 4.5 0.7 - - + -
119G TYR 3.4 5.2 - - - +
120G GLN* 5.1 0.2 - - - -
130G SER* 5.6 1.1 - - - -
131G VAL* 1.4 74.0 - - - +
133G LEU* 1.3 61.0 + - - +
134G PHE 4.1 0.2 - - - -
172G VAL* 3.5 3.6 - - - -
173G ALA* 2.7 49.8 + - + +
180G PHE* 3.6 26.9 - - - -
182G CYS* 2.0 54.3 - - + -
185G ALA* 4.2 6.5 - - + -
186G PHE* 3.8 7.5 - - + -
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Residues in contact with LEU 133 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117G ALA 3.6 2.4 - - - +
118G VAL* 3.2 4.5 - - - -
119G TYR* 2.8 45.7 + - + +
121G LEU* 3.7 22.9 - - + +
131G VAL* 4.2 1.0 - - + -
132G CYS* 1.3 72.6 - - - +
134G PHE* 1.4 57.0 + - - +
135G THR* 3.8 29.7 + - + +
170G SER* 4.1 19.3 - - - +
171G ALA 3.7 2.0 - - - +
172G VAL* 3.8 25.1 - - + -
135H GLU* 4.9 1.8 - - - +
143H THR* 3.8 34.1 - - + +
145H VAL* 3.8 15.3 - - + -
194H ARG* 4.3 1.8 - - + -
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Residues in contact with PHE 134 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116G PRO* 4.5 4.0 - - + -
117G ALA 3.5 13.2 - - - -
118G VAL* 3.6 12.1 - - + -
133G LEU* 1.4 69.6 - - - +
135G THR* 1.3 59.4 + - - +
137G PHE* 3.2 40.1 - + + -
141G THR* 3.9 13.2 - - + -
142G ASN 5.7 0.7 - - - -
143G VAL* 4.5 12.1 - - + -
170G SER* 3.0 3.6 - - - -
171G ALA* 2.8 35.3 + - + +
186G PHE* 3.4 42.2 - + + -
189G SER* 5.9 0.7 - - - -
191G ILE* 3.8 19.1 - - + -
192G PRO* 3.8 24.0 - - + -
195G THR* 3.9 22.9 - - + -
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Residues in contact with THR 135 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116G PRO* 3.6 0.5 - - - +
117G ALA 3.0 29.5 + - - +
119G TYR* 3.6 37.5 - - + -
133G LEU* 3.8 22.1 - - + +
134G PHE* 1.3 75.3 - - - +
136G ASP* 1.4 87.5 + - - +
137G PHE* 3.2 8.9 + - - -
168G SER* 4.5 1.6 + - - -
169G ASN 3.3 13.3 + - - -
170G SER* 4.1 5.9 - - - -
135H GLU* 5.1 0.2 - - - +
143H THR* 5.2 0.3 + - - -
196H ARG* 3.9 13.6 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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