Contacts of the strand formed by residues 94 - 98 (chain D) 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 ALA 94 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D ARG 3.3 8.6 + - - +
93D PRO* 1.3 75.5 - - - +
95D PHE* 1.3 63.5 + - - +
116D THR* 4.0 1.2 - - - +
117D ASN* 3.5 1.6 + - - -
118D GLN* 2.8 30.7 + - - +
121D PRO* 4.5 2.9 - - - +
129D PHE* 6.1 0.2 - - - -
216D GLY 3.5 7.2 - - - -
217D PHE* 4.0 14.4 - - + +
140E LEU* 4.2 13.5 - - + -
186E VAL* 3.9 21.1 - - + -
220E LEU* 4.5 3.1 - - + -
221E PHE* 4.2 5.8 - - + -
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Residues in contact with PHE 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D ALA* 1.3 77.1 - - - +
96D SER* 1.3 73.9 + - - +
97D ALA 4.1 1.3 - - - -
116D THR* 3.2 14.4 - - - +
117D ASN* 3.7 15.7 - - - +
121D PRO* 4.7 1.3 - - + -
122D TYR* 3.7 32.8 - + + -
129D PHE* 3.6 34.3 - + + -
139D PHE* 3.9 4.9 - + - -
214D PHE* 3.3 48.7 - + - -
215D SER* 3.4 12.1 - - - -
216D GLY* 2.9 54.6 + - - +
186E VAL* 3.5 8.9 - - - +
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Residues in contact with SER 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D PHE* 1.3 73.4 + - - +
97D ALA* 1.3 62.6 + - - +
114D VAL* 3.8 1.4 - - - +
115D ILE* 2.9 26.8 + - - -
116D THR* 3.0 13.3 + - - +
213D VAL* 4.4 1.3 - - - -
214D PHE 3.3 6.7 - - - -
215D SER* 2.4 25.3 + - - -
185E MET* 3.5 24.5 - - - -
186E VAL 2.8 29.2 + - - -
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Residues in contact with ALA 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D PHE* 4.5 1.8 - - + -
96D SER* 1.3 75.6 - - - +
98D ILE* 1.3 65.4 + - - +
111D PHE* 3.5 18.7 - - + +
113D THR 3.4 8.5 - - - +
114D VAL* 4.4 3.8 - - - -
115D ILE 4.3 0.7 - - - +
122D TYR* 3.4 37.0 - - + -
213D VAL* 3.3 3.5 - - - +
214D PHE 2.8 35.0 + - - +
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Residues in contact with ILE 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D ALA* 1.3 79.8 - - - +
99D ARG* 1.3 63.5 + - - +
100D ARG* 3.3 39.9 - - - +
111D PHE* 3.3 5.6 - - - -
112D ASP 3.2 7.1 + - - -
113D THR* 2.7 51.5 + - + +
115D ILE* 3.7 31.2 - - + -
211D ASP* 3.7 7.9 - - - +
212D SER 3.1 15.0 - - - +
213D VAL* 4.1 12.6 - - + -
167E VAL 4.9 0.7 - - - +
168E VAL* 3.9 18.4 - - + -
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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