Contacts of the helix formed by residues 92 - 105 (chain A) in PDB entry 1NUS
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 92 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A TRP* 3.5 31.5 - - + +
91A MET* 1.3 78.3 - - - +
93A THR* 1.3 67.9 + - - +
94A VAL* 4.4 3.8 - - + +
95A LYS* 2.9 40.3 + - + +
96A VAL* 3.5 3.9 + - - +
149A LYS* 3.2 29.7 + - - -
152A HIS* 3.9 23.7 - - + +
401A NMN 3.4 16.6 - - - +
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Residues in contact with THR 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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12A CYS* 4.3 14.7 - - + +
84A GLU* 6.0 0.2 - - - -
91A MET 3.6 2.7 + - - -
92A GLU* 1.3 69.7 - - - +
94A VAL* 1.3 64.7 - - - +
96A VAL* 2.9 19.6 + - - +
97A LEU* 3.1 16.3 + - + +
132A LEU* 3.8 38.8 - - + -
148A TRP* 3.8 12.3 - - + -
156A ILE* 4.7 0.9 - - + -
401A NMN 3.0 48.0 + - - -
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Residues in contact with VAL 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A GLU* 4.4 1.9 - - + +
93A THR* 1.3 78.1 - - - +
95A LYS* 1.3 64.1 + - + +
97A LEU* 3.3 6.1 + - - +
98A ARG* 3.1 37.7 + - - +
152A HIS* 3.5 46.7 - - + +
155A GLU* 3.5 40.6 - - + +
156A ILE* 4.0 27.6 - - + +
160A PHE* 4.3 5.6 - - + -
401A NMN 4.6 1.0 + - - -
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Residues in contact with LYS 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A TRP* 4.9 0.3 - - - -
91A MET* 3.3 37.2 - - + +
92A GLU* 2.9 31.1 + - - +
94A VAL* 1.3 79.9 - - + +
96A VAL* 1.3 65.7 + - - +
98A ARG* 3.3 22.2 + - - +
99A HIS* 3.0 22.5 + - - +
152A HIS* 5.5 0.2 - - - -
301A SO4 2.9 37.5 + - - -
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Residues in contact with VAL 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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10A LEU* 4.0 11.0 - - + -
12A CYS* 4.1 7.9 - - - -
47A SER* 4.1 3.1 - - - +
83A TRP* 4.3 9.2 - - + -
84A GLU* 3.6 46.7 - - + +
91A MET* 3.9 19.3 - - + +
92A GLU 4.0 9.0 - - - +
93A THR* 2.9 11.2 + - - +
95A LYS* 1.3 77.3 - - - +
97A LEU* 1.3 63.4 + - - +
99A HIS* 3.3 1.0 + - - +
100A HIS* 3.0 47.2 + - + +
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Residues in contact with LEU 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 3.7 22.9 - - + -
93A THR* 3.1 16.6 + - + +
94A VAL* 3.5 7.9 - - - +
96A VAL* 1.3 77.2 - - - +
98A ARG* 1.3 51.7 + - - +
100A HIS 3.2 0.9 + - - -
101A HIS* 2.7 37.1 + - - +
130A LEU* 3.3 26.3 - - + +
132A LEU* 4.2 36.1 - - + +
156A ILE* 4.0 25.1 - - + -
160A PHE* 3.8 39.7 - - + -
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Residues in contact with ARG 98 (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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94A VAL* 3.1 33.9 + - - +
95A LYS* 3.6 24.6 - - - +
97A LEU* 1.3 75.3 - - - +
99A HIS* 1.3 57.4 + - - +
101A HIS* 3.2 5.2 + - - +
102A SER* 2.8 34.6 + - - +
152A HIS* 4.4 1.2 + - - -
155A GLU* 2.7 43.9 + - - +
160A PHE* 3.8 12.1 - - + -
301A SO4 2.9 41.4 + - - -
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Residues in contact with HIS 99 (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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83A TRP* 3.1 73.9 - + + +
95A LYS 3.0 14.2 + - - +
96A VAL 3.5 6.5 - - - +
98A ARG* 1.3 75.9 - - - +
100A HIS* 1.3 78.8 + + - +
102A SER* 3.2 8.9 + - - -
103A LYS* 2.9 40.1 + - + +
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Residues in contact with HIS 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 4.2 15.0 - - + +
45A ILE* 4.0 21.3 - - + +
47A SER* 4.6 5.1 + - - -
81A ASP* 3.1 43.9 + - + +
83A TRP* 4.6 4.6 - - - +
96A VAL* 3.0 45.4 + - + +
99A HIS* 1.3 91.3 - + - +
101A HIS* 1.3 64.9 + - - +
103A LYS* 3.4 15.1 + - + +
104A LEU* 3.1 26.2 + - + +
130A LEU* 3.7 22.2 - - + -
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Residues in contact with HIS 101 (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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97A LEU 2.7 22.6 + - - +
98A ARG* 3.4 6.3 - - - +
99A HIS 3.1 0.2 - - - -
100A HIS* 1.3 70.3 - - - +
102A SER* 1.3 67.1 + - - +
104A LEU* 3.1 19.4 + - - +
105A LEU* 3.2 33.9 + - + +
127A VAL* 4.2 22.2 - - + -
128A PRO 4.6 6.8 + - - -
129A GLU* 5.9 0.7 - - - -
130A LEU* 3.7 17.6 + - + +
159A LYS 5.7 3.1 - - - -
160A PHE* 3.7 24.9 - + + -
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Residues in contact with SER 102 (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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98A ARG* 2.8 17.9 + - - +
99A HIS* 3.5 10.2 - - - -
101A HIS* 1.3 76.8 - - - +
103A LYS* 1.3 66.7 + - - +
105A LEU* 3.0 36.6 + - - +
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Residues in contact with LYS 103 (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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79A ARG* 4.0 17.2 - - - +
81A ASP* 3.1 24.2 + - - -
83A TRP* 6.0 0.6 - - - +
99A HIS* 2.9 27.3 + - + +
100A HIS* 3.4 26.2 - - - +
101A HIS 3.1 0.4 - - - -
102A SER* 1.3 78.3 - - - +
104A LEU* 1.3 64.0 + - + +
105A LEU 3.2 5.9 + - - +
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Residues in contact with LEU 104 (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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8A VAL* 3.7 36.6 - - + -
42A ILE* 5.6 2.7 - - + -
43A GLN* 5.4 4.9 - - - +
45A ILE* 6.3 1.8 - - + -
100A HIS* 3.1 15.6 + - + +
101A HIS* 3.1 12.0 + - - +
103A LYS* 1.3 79.7 - - + +
105A LEU* 1.3 62.1 + - - +
127A VAL* 4.8 8.7 - - + +
128A PRO* 4.0 36.9 - - + +
130A LEU* 4.2 22.4 - - + -
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Residues in contact with LEU 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A HIS* 3.6 27.1 - - + +
102A SER* 3.0 32.5 + - - +
103A LYS 3.9 4.9 - - - +
104A LEU* 1.3 85.0 - - - +
127A VAL* 3.7 35.9 - - + -
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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