Contacts of the strand formed by residues 188 - 197 (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 GLU 188 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129C LYS* 3.2 36.4 + - + +
130C PHE 3.2 6.7 - - - +
131C THR* 4.0 17.8 + - + +
156C ARG* 3.4 3.6 - - - +
157C SER* 2.8 37.2 + - - +
186C GLY 3.9 9.9 - - - +
187C GLU* 1.3 76.2 - - - +
189C VAL* 1.3 64.1 + - - +
190C TRP* 3.7 19.9 - - + -
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Residues in contact with VAL 189 (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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128C GLY 4.6 0.2 - - - +
129C LYS* 3.8 0.9 - - - -
130C PHE* 2.9 46.8 + - + +
140C PHE* 3.8 40.4 - - + -
154C LEU* 4.2 20.4 - - + -
155C TYR 3.2 12.8 - - - +
156C ARG* 4.5 7.0 - - + -
181C LEU* 4.8 1.8 - - + -
183C LEU* 3.9 24.7 - - + -
187C GLU 5.2 0.2 - - - +
188C GLU* 1.3 79.0 - - - +
190C TRP* 1.3 68.3 + - - +
209C PHE* 4.4 6.9 - - + -
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Residues in contact with TRP 190 (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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109C LEU* 3.6 30.2 - - + +
128C GLY 3.7 18.6 - - - +
129C LYS* 4.0 20.0 - - + -
154C LEU* 3.5 4.0 - - - +
155C TYR* 2.7 71.3 + + + +
157C SER* 4.2 1.6 - - - -
158C GLY* 3.4 29.2 - - - -
188C GLU* 3.7 41.1 - - + -
189C VAL* 1.3 84.9 - - - +
191C LEU* 1.3 74.8 + - - +
192C ALA* 4.5 3.9 - - + +
209C PHE* 4.7 5.8 - - - -
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Residues in contact with LEU 191 (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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109C LEU* 3.6 5.7 - - - +
110C ILE* 2.7 44.9 + - + +
112C PHE* 4.0 17.7 - - + -
128C GLY 5.1 0.6 + - - -
142C TYR* 3.7 38.4 - - + -
152C VAL* 4.0 13.5 - - + -
153C LEU 3.2 4.3 - - - +
154C LEU* 3.7 40.8 - - + -
190C TRP* 1.3 79.4 - - - +
192C ALA* 1.3 56.4 + - - +
209C PHE* 3.8 31.2 - - + -
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Residues in contact with ALA 192 (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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108C SER 3.2 19.5 - - - +
109C LEU* 4.0 3.6 - - - +
110C ILE* 3.7 5.5 - - - +
152C VAL* 3.4 5.7 - - - -
153C LEU* 2.7 35.0 + - + +
155C TYR* 4.0 27.4 - - + -
190C TRP* 4.5 4.3 - - + +
191C LEU* 1.3 74.7 - - - +
193C VAL* 1.3 67.8 + - - +
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Residues in contact with VAL 193 (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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104C PRO* 4.2 10.1 - - + -
105C ALA 3.4 25.1 - - - +
107C ASN* 3.2 18.2 - - - -
108C SER 2.9 17.0 + - - +
110C ILE* 3.5 25.6 - - + -
150C LEU* 3.7 19.1 - - + -
151C CYS 3.3 17.3 - - - +
153C LEU* 4.2 7.3 - - - +
192C ALA* 1.3 77.3 - - - +
194C ASN* 1.3 62.4 + - - +
196C TYR 3.8 6.7 - - - +
197C TYR* 3.5 20.9 - - + +
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Residues in contact with ASN 194 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210B GLY* 6.3 0.2 - - - -
106C PRO* 3.5 5.5 - - - +
107C ASN* 2.7 39.8 + - - +
151C CYS* 3.4 31.9 + - - +
153C LEU* 4.0 17.3 - - + +
163C THR* 4.8 4.2 - - - +
193C VAL* 1.3 79.3 - - - +
195C ASP* 1.3 64.5 + - - +
196C TYR* 2.8 35.5 + - - +
197C TYR* 4.0 0.9 - - - +
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Residues in contact with ASP 195 (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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106C PRO* 4.6 6.7 - - - +
107C ASN* 2.6 30.6 + - - +
194C ASN* 1.3 82.7 + - - +
196C TYR* 1.3 69.3 + - + +
197C TYR* 3.2 21.2 - - - -
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Residues in contact with TYR 196 (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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149C ASN* 3.5 44.3 + - + +
150C LEU* 3.6 0.2 - - - -
151C CYS* 3.0 47.4 + - - +
167C HIS* 3.4 35.3 - + - -
193C VAL* 3.8 2.4 - - - +
194C ASN* 2.8 14.3 + - - +
195C ASP* 1.3 85.5 - - + +
197C TYR* 1.3 58.4 + - - +
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Residues in contact with TYR 197 (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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103C PRO* 4.1 18.4 - - + -
104C PRO* 2.9 47.9 - - - +
106C PRO* 4.0 29.4 - - + -
149C ASN 3.4 1.4 + - - -
150C LEU* 3.9 3.7 - - - +
193C VAL* 3.5 27.8 - - + -
194C ASN 4.0 4.0 - - - +
195C ASP 3.2 19.5 - - - -
196C TYR* 1.3 74.1 - - - +
198C ASP* 1.3 70.8 + - + +
199C MET* 4.0 1.4 - - - +
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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