Contacts of the strand formed by residues 135 - 138 (chain G) in PDB entry 5JLH
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 TYR 135 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128G ARG* 3.3 19.2 + - - -
133G LEU* 4.5 3.3 - - - +
134G ILE* 1.3 106.3 - - + +
136G THR* 1.3 69.1 + - - +
142G CYS* 4.4 8.5 - - - -
143G VAL 3.4 2.7 - - - -
144G VAL* 3.4 31.9 - - + +
153G ILE* 5.5 1.8 - - + -
154G TYR* 2.6 27.6 + + - -
172G PRO* 3.1 36.0 - - + +
173G HIS* 3.4 31.2 - + - -
174G VAL* 3.3 35.7 - - + +
207G ASN* 3.7 8.1 + - - -
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Residues in contact with THR 136 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107G ALA 4.1 2.5 - - - +
108G GLU 3.6 10.5 - - - +
110G MET* 3.8 13.5 - - + -
124G ASN* 4.2 3.6 - - - +
125G LEU* 3.6 29.5 - - + +
128G ARG* 3.3 32.4 + - - +
133G LEU 5.1 0.3 + - - -
134G ILE 5.0 0.9 + - - -
135G TYR* 1.3 78.2 + - - +
137G TYR* 1.3 69.6 + - - +
142G CYS* 3.6 2.3 - - - -
143G VAL* 2.6 42.9 + - - +
172G PRO* 3.9 7.9 - - - -
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Residues in contact with TYR 137 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108G GLU* 2.9 19.4 + - + +
109G ASP* 3.2 10.6 - - + +
110G MET* 2.7 36.1 + - - +
136G THR* 1.3 76.9 - - - +
138G SER* 1.3 53.8 + - - +
140G LEU 5.3 0.2 - - - -
141G PHE 3.4 9.6 - - - -
142G CYS* 4.0 14.6 - - - -
167G ARG* 3.4 62.1 + - + +
168G HIS* 6.0 0.4 - - - -
172G PRO* 3.5 35.1 - - + +
173G HIS 3.5 7.0 + - - -
176G ALA* 3.0 33.1 - - - +
177G VAL* 3.7 22.3 - - + +
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Residues in contact with SER 138 (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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110G MET* 3.5 32.3 - - - +
121G VAL* 5.2 0.2 - - - +
136G THR 4.0 2.0 + - - -
137G TYR* 1.3 70.8 - - - +
139G GLY* 1.3 66.8 + - - +
140G LEU 3.2 0.3 + - - -
141G PHE* 2.8 32.9 + - - +
143G VAL* 4.1 17.2 - - - +
721G VAL* 3.9 20.9 + - - +
725G ILE* 4.0 15.9 - - - +
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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