Contacts of the strand formed by residues 147 - 155 (chain D) in PDB entry 2JG7
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 HIS 147 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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456C ILE* 4.0 12.6 - - + +
142D SER* 3.4 26.8 + - - +
144D ARG* 3.3 44.1 + - + +
145D PRO* 2.8 25.5 + - + -
146D GLY* 1.3 78.7 - - - +
148D ALA* 1.3 60.3 + - - +
494D THR* 3.8 17.5 - - + -
495D ILE 3.2 4.3 - - - +
496D ASN* 3.5 39.1 - - + +
497D TYR* 3.5 7.4 + - - -
498D SER* 4.5 3.1 - - - -
500D ASP* 5.9 2.0 - - + -
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Residues in contact with ALA 148 (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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439B PHE* 3.5 37.7 - - + -
139D VAL* 6.3 1.3 - - + -
142D SER* 4.7 0.4 - - - -
147D HIS* 1.3 73.5 - - - +
149D LEU* 1.3 61.3 + - - +
150D ILE* 4.2 6.5 - - + -
493D CYS 3.7 0.3 - - - +
494D THR* 3.3 4.7 - - - +
495D ILE* 2.7 51.9 + - + +
497D TYR* 3.6 4.1 - - + -
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Residues in contact with LEU 149 (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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462C GLU* 3.9 33.2 - - + +
464C GLY* 5.0 2.5 - - - -
465C GLY 4.6 8.1 - - - +
139D VAL* 3.9 2.2 - - - +
140D LEU* 2.8 68.3 + - + +
141D PRO 4.5 2.7 - - - +
142D SER* 3.9 16.4 - - - -
147D HIS 4.1 1.0 + - - -
148D ALA* 1.3 75.1 - - - +
150D ILE* 1.3 66.5 + - - +
492D THR* 3.8 24.5 - - + -
493D CYS 3.3 10.1 - - - +
494D THR* 3.3 23.8 - - - +
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Residues in contact with ILE 150 (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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139A VAL* 4.1 14.8 - - + -
150A ILE* 5.5 9.9 - - + -
439B PHE* 6.1 2.2 - - + -
439C PHE* 5.4 7.9 - - + -
442C LEU* 4.0 17.5 - - + -
138D PRO 3.9 4.0 - - - -
139D VAL* 3.9 23.6 - - + -
140D LEU* 4.6 2.9 - - - +
148D ALA* 4.2 7.8 - - + -
149D LEU* 1.3 86.1 - - - +
151D GLU* 1.3 59.8 + - - +
152D GLN* 3.7 30.7 - - + +
492D THR* 3.8 1.7 - - - -
493D CYS* 2.8 51.7 + - + +
495D ILE* 4.9 7.6 - - + -
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Residues in contact with GLU 151 (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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139A VAL* 4.0 9.2 - - - +
466C ALA* 4.5 1.6 + - - +
481C SER* 2.7 22.2 + - - -
482C ASP* 5.8 0.3 - - - -
137D GLY* 3.5 21.8 + - - +
138D PRO* 3.0 37.9 + - + +
140D LEU* 4.9 6.5 - - + +
150D ILE* 1.3 71.7 - - - +
152D GLN* 1.3 63.3 + - - +
153D TRP* 2.8 25.2 + - - +
485D LYS* 5.6 1.4 + - - -
490D ARG* 2.6 52.1 + - + -
491D SER 3.5 5.4 - - - +
492D THR* 4.8 6.1 + - + +
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Residues in contact with GLN 152 (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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139A VAL* 3.5 27.5 - - - +
442C LEU* 3.3 31.8 + - + +
443C GLY* 4.4 5.3 - - - -
150D ILE* 3.7 24.1 + - + +
151D GLU* 1.3 72.5 - - - +
153D TRP* 1.3 67.4 + - - +
154D ASN* 4.2 9.5 + - - +
489D ARG 3.6 0.7 - - - +
490D ARG* 3.5 4.3 - - - +
491D SER* 2.8 50.9 + - - +
493D CYS* 4.0 10.8 - - - -
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Residues in contact with TRP 153 (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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135D ILE 5.7 0.2 - - - -
136D GLY* 3.4 13.5 + - - -
137D GLY* 3.3 29.1 - - - +
151D GLU* 2.8 23.4 + - - -
152D GLN* 1.3 81.9 + - - +
154D ASN* 1.3 67.0 + - - +
155D PRO* 4.9 0.2 - - - +
484D TRP* 3.7 24.0 - + + -
485D LYS* 3.6 49.2 - - + +
488D MET* 3.7 34.2 - - + +
489D ARG 3.5 2.5 - - - -
490D ARG* 3.6 68.4 - - + -
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Residues in contact with ASN 154 (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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442C LEU 3.2 24.2 + - - -
443C GLY* 3.3 5.4 + - - -
444C PRO* 3.0 36.0 - - + +
152D GLN* 4.2 12.4 + - - +
153D TRP* 1.3 80.3 + - - +
155D PRO* 1.4 72.4 - - + +
488D MET* 3.2 9.2 - - - +
489D ARG* 2.8 64.9 + - + +
491D SER* 4.5 3.2 + - - -
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Residues in contact with PRO 155 (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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444C PRO* 4.1 11.4 - - + -
70D TRP* 3.8 21.7 - - + +
74D ALA* 4.6 5.8 - - + -
81D ARG* 4.5 8.5 - - - +
154D ASN* 1.4 95.1 - - + +
156D VAL* 1.3 63.3 + - - +
182D CYS 3.2 22.0 - - - +
183D GLY* 3.1 30.3 - - - +
184D ASN* 3.3 11.0 - - - +
487D TYR 4.3 2.0 - - - +
488D MET* 3.7 3.3 - - + -
489D ARG* 3.9 14.4 + - - -
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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