Contacts of the helix formed by residues 89 - 97 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A LEU* 3.7 13.0 - - + -
73A LEU* 2.8 36.3 - - + +
76A PHE* 3.3 31.0 - - + +
77A THR* 4.0 4.7 - - - +
80A VAL* 3.6 39.3 - - + -
86A VAL* 3.1 12.0 + - + +
88A CYS* 1.3 77.8 - - - +
90A LEU* 1.3 68.8 + - - +
91A PRO 3.6 0.2 - - - -
92A PRO* 3.0 16.9 - - - +
93A LEU* 3.4 13.6 - - + +
115A ILE* 3.9 21.3 - - + -
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Residues in contact with LEU 90 (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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87A HIS* 3.7 13.5 - - - +
88A CYS 3.1 0.2 - - - -
89A LEU* 1.3 81.9 - - - +
91A PRO* 1.3 75.8 - - + +
93A LEU* 2.8 2.9 + - - -
94A GLU* 2.8 25.0 + - - +
112A LEU* 3.6 17.0 - - + -
115A ILE* 4.0 10.5 - - + -
119A HIS* 3.7 23.8 - - + -
127A HIS* 3.7 36.3 - - + +
128A PHE* 3.8 17.0 - - + +
131A LEU* 3.5 25.6 - - + -
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Residues in contact with PRO 91 (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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56A THR* 4.1 22.1 - - + +
87A HIS 3.9 6.5 - - - +
88A CYS* 3.5 14.4 - - - +
89A LEU 3.7 0.2 - - - -
90A LEU* 1.3 94.2 - - + +
92A PRO* 1.3 66.1 - - + +
94A GLU* 3.7 12.0 + - + +
95A SER* 3.5 20.1 + - - -
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Residues in contact with PRO 92 (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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52A LEU* 5.2 7.4 - - + +
55A LEU* 4.3 22.4 - - + +
56A THR* 4.0 19.1 - - - +
69A LEU* 5.3 3.4 - - + -
73A LEU* 3.6 25.6 - - + -
88A CYS 4.1 4.3 - - - +
89A LEU* 3.0 28.0 - - - +
91A PRO* 1.3 88.0 - - + +
93A LEU* 1.3 64.4 + - - +
95A SER* 2.9 10.0 + - - -
96A LEU* 2.8 30.2 + - - +
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Residues in contact with LEU 93 (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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70A ALA* 3.9 18.6 - - - +
73A LEU* 3.3 39.5 - - + +
89A LEU* 3.4 17.5 - - + +
90A LEU 2.8 9.5 + - - +
92A PRO* 1.3 69.1 - - - +
94A GLU* 1.3 53.0 + - - +
95A SER 2.9 4.5 - - - -
96A LEU* 2.9 7.8 + - + +
97A ALA* 2.7 35.8 + - - +
108A ALA* 4.2 8.9 - - - +
111A SER* 4.0 20.0 - - - -
112A LEU* 3.6 31.9 - - + -
115A ILE* 3.7 19.1 - - + -
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Residues in contact with GLU 94 (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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90A LEU* 2.8 12.5 + - - +
91A PRO* 3.8 13.3 - - - +
93A LEU* 1.3 76.0 - - - +
95A SER* 1.3 60.2 + - - +
97A ALA* 3.4 16.2 - - - +
98A THR* 3.5 10.9 + - - -
112A LEU* 5.1 0.2 - - - -
131A LEU* 3.5 40.5 - - + +
134A ARG* 3.2 47.4 + - - +
135A LEU* 4.1 12.4 - - + +
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Residues in contact with SER 95 (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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56A THR 5.4 4.3 + - - -
91A PRO 3.5 10.5 + - - -
92A PRO* 2.9 12.7 + - - -
94A GLU* 1.3 77.7 - - - +
96A LEU* 1.3 62.3 + - - +
97A ALA 2.9 4.9 - - - -
98A THR* 2.9 22.5 + - - -
99A VAL* 3.4 7.3 + - - +
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Residues in contact with LEU 96 (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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66A LEU* 3.3 47.6 - - + +
69A LEU* 3.6 33.0 - - + -
70A ALA* 3.7 17.9 - - + -
73A LEU* 4.1 8.7 - - + -
92A PRO 2.8 17.1 + - - +
93A LEU* 2.9 9.4 + - - +
95A SER* 1.3 76.7 - - - +
97A ALA* 1.3 59.4 + - - +
99A VAL* 3.0 22.8 - - + +
104A VAL* 3.7 14.5 - - + +
105A ARG* 3.4 15.4 - - - -
108A ALA* 3.5 13.5 - - + -
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Residues in contact with ALA 97 (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 LEU 2.7 15.2 + - - +
94A GLU* 3.4 11.4 - - - +
95A SER 2.9 0.4 - - - -
96A LEU* 1.3 79.3 - - - +
98A THR* 1.3 56.5 + - - +
105A ARG* 3.2 15.5 - - - +
108A ALA* 3.6 12.3 - - + +
109A VAL* 5.1 2.7 - - + -
112A LEU* 5.0 6.7 - - + -
135A LEU* 3.7 27.8 - - + -
143A SER* 4.6 2.9 - - - -
146A SER* 3.1 28.0 + - - +
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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