Contacts of the strand formed by residues 93 - 101 (chain D) in PDB entry 1NJI
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 GLY 93 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2674A G 3.7 14.1 - - - -
2675A A 6.1 0.4 - - - -
89D ASP* 5.0 1.1 - - - -
90D THR* 2.9 38.7 + - - -
91D PRO 3.5 0.8 - - - -
92D TYR* 1.3 77.1 - - - +
94D GLN* 1.3 66.0 + - - -
95D ARG* 4.8 0.2 - - - -
144K THR* 3.8 7.3 + - - -
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Residues in contact with GLN 94 (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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2673A U 2.5 41.2 + - - +
2674A G 3.2 15.4 + - - +
87D TYR* 4.1 14.0 - - + -
88D GLU 3.5 6.7 - - - +
89D ASP* 3.6 22.4 + - - +
93D GLY* 1.3 76.0 - - - -
95D ARG* 1.3 62.2 + - - +
138D GLY* 4.0 1.2 - - - -
139D ASP* 3.1 40.8 + - - +
141D ARG* 3.6 15.4 + - - -
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Residues in contact with ARG 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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2673A U 4.3 5.6 + - - +
2811A A 5.7 3.6 - - - +
2817A G 3.5 26.6 + - - +
2818A A 3.9 29.3 - - - +
87D TYR* 3.2 5.2 - - - -
88D GLU* 2.8 36.5 + - + +
90D THR* 4.3 20.9 + - + -
92D TYR* 3.7 36.2 + - - +
93D GLY 4.3 6.3 - - - +
94D GLN* 1.3 83.4 - - - +
96D PRO* 1.3 75.2 - - + +
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Residues in contact with PRO 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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2672A C 3.8 10.1 - - - +
2673A U 4.8 4.7 - - - +
2817A G 5.0 0.9 - - - +
2818A A 2.9 51.7 + - + +
2819A C 3.1 34.0 - - - +
85D ARG* 3.9 17.3 - - + +
86D ALA 3.5 6.1 - - - +
87D TYR* 3.6 24.7 - - + -
88D GLU* 5.5 1.6 - - - +
94D GLN 4.7 0.9 - - - +
95D ARG* 1.3 83.5 - - + +
97D LEU* 1.3 61.1 + - - +
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Residues in contact with LEU 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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2819A C 3.1 23.5 - - - +
2820A A 4.0 0.7 + - - -
86D ALA* 2.5 27.3 + - + +
87D TYR 4.5 6.3 - - - +
88D GLU* 4.0 30.1 - - + +
95D ARG 3.3 1.6 + - - -
96D PRO* 1.3 72.3 - - - +
98D THR* 1.3 75.9 + - - +
127D GLN* 3.6 30.2 + - + +
128D ILE* 4.5 7.2 - - - -
131D ALA* 3.5 32.5 - - + -
137D LEU* 5.0 1.6 - - + -
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Residues in contact with THR 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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2819A C 3.9 7.2 - - - -
2820A A 3.0 28.0 - - - +
84D LEU 4.0 0.3 - - - +
85D ARG* 4.1 1.2 - - - +
86D ALA* 2.9 26.9 + - - +
97D LEU* 1.3 81.2 - - - +
99D GLU* 1.3 74.2 + - - +
119D HIS* 6.1 0.2 - - + -
124D ALA* 4.2 25.8 - - + -
127D GLN* 2.7 39.6 + - - +
128D ILE* 4.4 6.7 - - - +
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Residues in contact with GLU 99 (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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2670A G 4.7 2.1 + - - -
2819A C 2.4 22.6 + - - +
2820A A 2.9 24.0 - - - +
83D ALA* 4.9 0.9 - - + -
84D LEU 3.3 5.8 - - - +
85D ARG* 2.7 49.5 + - + +
98D THR* 1.3 86.3 - - - +
100D VAL* 1.3 65.8 + - - +
101D TRP* 3.0 36.5 + - + +
119D HIS* 3.2 22.5 + - - -
124D ALA* 3.2 8.2 - - - +
143D ILE* 4.6 6.1 - - + +
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Residues in contact with VAL 100 (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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83D ALA* 3.0 5.4 - - - -
84D LEU* 2.9 36.2 + - + +
99D GLU* 1.3 76.3 - - - +
101D TRP* 1.3 69.2 + - - +
119D HIS* 3.8 2.2 - - - -
121D PRO* 4.2 19.1 - - + +
124D ALA* 3.8 16.4 - - + -
125D GLU* 4.0 13.5 - - + +
128D ILE* 4.1 15.5 - - + -
179D LEU* 3.9 32.1 - - + -
182D VAL* 3.8 5.6 - - + +
183D GLU* 4.3 12.6 - - - +
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Residues in contact with TRP 101 (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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2670A G 6.1 1.3 - - - -
2820A A 3.2 25.9 + - - -
82D VAL* 3.3 39.0 - - + -
83D ALA* 3.5 14.3 - - + +
99D GLU* 3.0 38.2 + - + +
100D VAL* 1.3 85.0 - - - +
102D THR* 1.3 70.6 + - - +
105D PHE* 4.0 9.9 - + - -
109D LEU* 5.1 0.7 - - + -
113D LEU* 4.1 27.8 - - + -
116D PRO* 4.0 24.7 - - + -
119D HIS* 3.1 32.8 + + + -
121D PRO* 4.0 17.0 - - - +
143D ILE* 4.5 17.7 - - + -
182D VAL* 4.4 0.2 - - - -
183D GLU* 4.3 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