Contacts of the strand formed by residues 93 - 97 (chain C) in PDB entry 2JG8
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 93 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A TYR* 3.9 19.5 - - + -
184A VAL* 3.7 29.4 - - + -
219A ILE* 3.9 7.2 - - + -
220A PHE* 4.0 15.7 - - + -
92C SER* 1.3 77.2 + - - +
94C PHE* 1.3 71.1 + - - +
117C THR* 4.4 2.7 - - - +
118C ASN* 3.8 3.1 - - - +
119C PRO* 3.4 37.3 - - + +
120C GLN* 3.3 6.0 + - - +
122C ASP* 4.8 2.2 + - - +
211C GLY 3.4 5.8 - - - -
212C PHE* 3.5 21.1 - - + -
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Residues in contact with PHE 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A VAL* 3.9 3.6 - - - +
92C SER* 5.4 0.2 - - - -
93C VAL* 1.3 80.4 - - - +
95C THR* 1.3 68.6 + - - +
96C VAL* 4.1 7.0 - - + -
117C THR* 3.2 14.8 - - - +
118C ASN* 3.5 20.0 - - - +
122C ASP* 5.1 1.8 - - + -
123C TYR* 3.9 31.2 - + + -
130C PHE* 3.5 35.9 - + + -
140C PHE* 4.2 4.5 - + - -
209C PHE* 3.5 45.1 - + - -
210C SER* 3.4 5.2 - - - -
211C GLY* 3.0 58.1 + - - +
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Residues in contact with THR 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A MET* 4.0 7.0 - - + -
184A VAL* 2.9 24.8 + - - +
94C PHE* 1.3 72.3 + - - +
96C VAL* 1.3 61.4 + - - +
116C LEU* 2.8 53.6 + - + -
117C THR* 2.9 17.4 + - - +
208C VAL* 3.2 32.3 - - + -
209C PHE 3.5 4.9 - - - -
210C SER* 2.8 16.2 + - - +
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Residues in contact with VAL 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C PHE* 4.1 10.8 - - + -
95C THR* 1.3 79.4 - - - +
97C THR* 1.3 61.5 + - - +
112C PHE* 3.5 27.7 - - + +
114C ALA 3.2 13.9 - - - +
115C VAL* 4.1 18.2 - - + +
116C LEU* 5.1 0.7 - - - -
118C ASN* 5.1 0.9 - - + -
123C TYR* 3.6 41.1 - - + -
125C THR* 4.8 0.9 - - + -
208C VAL* 3.3 7.8 - - - +
209C PHE* 3.0 42.6 + - + +
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Residues in contact with THR 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A LEU* 3.9 17.4 - - + +
96C VAL* 1.3 77.3 - - - +
98C ARG* 1.3 68.5 + - - +
99C GLN 3.6 0.2 + - - -
112C PHE* 3.5 6.9 - - - +
113C ASN 3.2 6.4 + - - -
114C ALA* 2.7 49.7 + - + +
116C LEU* 4.9 9.6 - - + -
207C SER 2.8 17.9 + - - -
99F GLN* 2.6 41.9 + - - +
114F ALA* 4.8 4.3 - - + -
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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