Contacts of the helix formed by residues 89 - 97 (chain D) in PDB entry 2NYM
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 LEU 89 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D LEU* 3.6 23.6 - - + -
73D LEU* 3.0 35.2 - - + +
76D PHE* 3.6 33.9 - - + +
77D THR* 4.1 5.8 - - - +
80D VAL* 3.7 24.7 - - + -
86D VAL* 3.1 12.2 + - + +
88D CYS* 1.3 79.9 - - - +
90D LEU* 1.3 67.9 + - - +
91D PRO 3.5 0.2 - - - -
92D PRO* 2.9 18.9 - - - +
93D LEU* 3.6 11.3 - - + +
115D ILE* 3.8 22.4 - - + -
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Residues in contact with LEU 90 (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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87D HIS* 3.9 9.6 - - - +
89D LEU* 1.3 76.3 - - - +
91D PRO* 1.3 60.8 - - + +
93D LEU* 2.8 28.4 + - - +
94D GLU* 2.8 18.5 + - - +
112D LEU* 4.0 14.4 - - + -
115D ILE* 3.8 21.5 - - + -
119D HIS* 3.7 15.9 - - + -
127D HIS* 3.8 17.0 - - + +
128D PHE* 3.7 50.7 - - + +
131D LEU* 4.2 14.0 - - + +
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Residues in contact with PRO 91 (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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56D THR* 3.8 23.8 - - + +
87D HIS 4.0 7.2 - - - +
88D CYS* 3.8 10.1 - - - +
89D LEU 3.7 1.8 - - - -
90D LEU* 1.3 95.3 - - + +
92D PRO* 1.3 65.7 - - + +
94D GLU* 3.8 11.0 + - + +
95D SER* 3.6 21.0 + - - -
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Residues in contact with PRO 92 (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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52D LEU* 5.1 7.9 - - + -
55D LEU* 4.4 20.9 - - + +
56D THR* 3.6 19.5 - - - +
69D LEU* 5.6 2.0 - - + +
73D LEU* 3.7 26.7 - - + -
88D CYS 4.2 4.7 - - - +
89D LEU* 2.9 31.9 - - - +
91D PRO* 1.3 89.1 - - + +
93D LEU* 1.3 59.2 + - - +
94D GLU 3.3 0.4 - - - -
95D SER* 3.4 7.8 + - - +
96D LEU* 3.1 31.6 + - + +
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Residues in contact with LEU 93 (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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70D ALA* 4.0 14.1 - - - +
73D LEU* 3.3 38.1 - - + +
89D LEU* 3.6 19.3 - - + +
90D LEU 2.8 7.4 + - - +
92D PRO* 1.3 70.8 - - - +
94D GLU* 1.3 57.9 + - - +
95D SER 3.0 1.6 - - - -
96D LEU* 3.1 10.2 + - + +
97D ALA* 2.7 36.6 + - - +
108D ALA* 4.1 8.6 - - - +
111D SER* 4.2 18.4 - - - -
112D LEU* 3.2 34.2 - - + +
115D ILE* 3.9 20.2 - - + -
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Residues in contact with GLU 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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90D LEU* 2.8 12.6 + - - +
91D PRO* 3.9 12.4 - - - +
93D LEU* 1.3 77.3 - - - +
95D SER* 1.3 60.3 + - - +
97D ALA* 3.7 14.9 + - - +
98D THR* 3.8 10.7 + - - -
112D LEU* 5.2 0.2 - - - -
131D LEU* 3.2 39.6 - - + +
134D ARG* 3.2 49.5 + - - +
135D LEU* 4.2 14.1 - - + +
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Residues in contact with SER 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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56D THR* 5.0 8.7 + - - +
91D PRO 3.6 12.0 + - - -
92D PRO* 3.4 10.9 + - - -
93D LEU 3.0 0.2 - - - -
94D GLU* 1.3 78.5 - - - +
96D LEU* 1.3 67.2 + - - +
98D THR* 2.9 23.0 + - - +
99D VAL* 3.5 6.0 + - - +
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Residues in contact with LEU 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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66D LEU* 3.3 47.6 - - + +
69D LEU* 3.9 19.1 - - + -
70D ALA* 3.7 29.8 - - + +
73D LEU* 4.1 8.5 - - + -
92D PRO 3.1 17.0 + - - +
93D LEU* 3.1 9.3 + - + +
95D SER* 1.3 77.9 - - - +
97D ALA* 1.3 61.4 + - - +
98D THR 3.0 1.0 + - - -
99D VAL* 3.0 28.6 + - + +
104D VAL* 4.3 3.1 - - + -
105D ARG* 3.3 12.5 - - - +
108D ALA* 3.5 14.6 - - + -
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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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93D LEU 2.7 19.8 + - - +
94D GLU* 3.8 8.7 - - - +
95D SER 3.1 0.4 - - - -
96D LEU* 1.3 72.9 - - - +
98D THR* 1.3 57.2 + - - +
105D ARG* 3.3 13.8 - - - +
108D ALA* 3.5 13.6 - - + +
109D VAL* 4.8 7.0 - - + -
112D LEU* 4.8 5.6 - - + -
135D LEU* 3.9 26.5 - - + -
142D THR 4.6 1.9 - - - +
143D SER* 4.7 1.4 - - - -
146D SER* 3.0 30.5 + - - +
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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