Contacts of the strand formed by residues 213 - 221 (chain A) 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 213 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A ALA 3.4 11.7 - - - +
98A ILE* 3.8 12.8 - - + -
111A PHE* 3.8 5.7 - - - -
141A PHE* 3.3 7.5 - - - +
142A GLN* 2.9 40.9 + - - +
211A ASP* 4.7 3.4 - - + -
212A SER* 1.3 80.3 - - - +
214A PHE* 1.3 64.4 + - - +
215A SER* 3.7 19.3 - - - +
168B VAL* 4.8 0.2 - - + -
170B PHE* 3.4 35.0 - - + -
184B GLY 3.9 4.5 - - - +
185B MET* 3.7 25.1 - - + -
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Residues in contact with PHE 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A PHE* 3.3 31.0 - + + -
96A SER* 3.4 0.7 - - - -
97A ALA 2.8 39.3 + - - +
111A PHE* 3.5 33.4 - + + -
122A TYR* 4.2 8.7 - + - -
127A GLY 4.2 15.7 - - - -
129A PHE* 5.2 0.7 - - + -
139A PHE* 4.3 21.3 - + + -
140A THR 3.4 13.9 - - - -
141A PHE* 4.3 1.3 - - + -
153A ILE* 4.9 6.3 - - + -
193A VAL* 4.5 9.0 - - + -
194A TRP* 4.3 14.6 - - - -
195A VAL* 3.7 30.1 - - + -
213A VAL* 1.3 73.6 - - - +
215A SER* 1.3 79.5 + - - +
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Residues in contact with SER 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A PHE* 3.3 12.8 - - - -
96A SER* 2.6 26.7 + - - -
139A PHE* 3.5 2.9 - - - -
140A THR* 3.0 47.3 + - - +
142A GLN* 5.4 1.7 + - - -
213A VAL* 3.7 10.4 - - - +
214A PHE* 1.3 80.8 + - - +
216A GLY* 1.3 60.3 + - - +
217A PHE* 5.6 0.9 - - - -
142B TYR* 4.6 5.1 - - - -
184B GLY 4.5 1.6 + - - -
185B MET* 4.3 4.0 + - - -
186B VAL* 4.2 11.6 + - - -
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Residues in contact with GLY 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A ALA* 3.4 0.9 - - - +
95A PHE* 2.9 50.5 + - - +
129A PHE* 5.5 2.5 - - - -
138A TYR 3.1 12.1 - - - -
139A PHE* 3.8 7.6 - - - -
215A SER* 1.3 75.4 - - - +
217A PHE* 1.3 68.8 + - - +
186B VAL* 4.4 0.7 - - - +
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Residues in contact with PHE 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A PRO 3.5 10.3 - - - +
94A ALA* 4.1 3.6 - - + -
129A PHE* 6.1 0.2 - - - -
137A TYR* 3.3 10.4 - - - -
138A TYR* 2.8 72.0 + + + -
139A PHE* 5.1 0.4 - - - -
140A THR* 5.6 1.6 - - + -
215A SER* 5.7 0.2 - - - -
216A GLY* 1.3 80.4 - - - +
218A LEU* 1.3 73.0 + - - +
219A ILE* 4.3 5.4 - - + -
142B TYR* 3.9 26.9 - + + -
186B VAL* 4.2 14.8 - - + -
218B PHE* 3.9 14.1 - + - -
220B LEU* 3.5 36.3 - - + -
221B PHE* 5.0 1.1 - - + -
139C TYR* 5.6 0.2 - + - -
212C PHE* 3.9 22.0 - + - -
214C LEU* 5.3 1.8 - - + -
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Residues in contact with LEU 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A PRO* 3.9 24.0 - - + +
93A PRO* 3.1 36.8 + - + +
133A VAL* 4.3 9.4 - - + +
135A GLY* 4.2 3.8 - - - -
136A TYR 3.4 18.4 - - - +
137A TYR* 3.5 38.1 - - + +
217A PHE* 1.3 81.0 - - - +
219A ILE* 1.3 60.1 + - - +
220A PHE* 3.6 20.4 - - - +
221A PRO* 3.9 15.5 - - + -
220B LEU* 5.2 1.6 - - - +
221B PHE* 3.4 23.6 - - + -
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Residues in contact with ILE 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A TYR 2.7 16.4 + - - +
137A TYR 3.9 3.1 - - - -
138A TYR* 3.7 28.9 - - + +
184A VAL* 3.9 18.4 - - + -
217A PHE* 4.2 9.0 - - + +
218A LEU* 1.3 76.0 - - - +
220A PHE* 1.3 78.0 + - + +
221B PHE* 5.4 5.0 - - - -
93C VAL* 3.9 7.0 - - + -
212C PHE* 3.6 50.9 - - + -
213C LEU 4.3 10.8 - - - +
214C LEU* 5.1 6.0 - - + +
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Residues in contact with PHE 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A TYR* 2.9 64.0 + + + -
218A LEU* 3.7 5.6 - - - -
219A ILE* 1.3 98.4 - - + +
221A PRO* 1.3 85.3 - - + +
222A SER* 5.5 1.3 - - - -
88C GLN* 5.5 6.1 - - + -
91C GLN* 3.6 56.5 - - + +
92C SER 4.7 3.6 - - - -
93C VAL* 4.0 24.0 - - + -
120C GLN* 4.2 11.7 - - - -
213C LEU 5.5 0.7 - - - -
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Residues in contact with PRO 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A PRO* 4.1 20.0 - - + -
133A VAL* 4.2 16.6 - - + -
134A PRO 3.4 14.8 - - - +
135A GLY* 3.9 0.4 - - - -
218A LEU* 3.9 12.3 - - + -
220A PHE* 1.3 102.2 - - + +
222A SER* 1.3 65.9 + - - +
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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