Contacts of the helix formed by residues 83 - 91 (chain A) in PDB entry 1NUE
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 VAL 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A GLU* 3.3 34.9 + - + +
6A ARG* 3.8 15.5 - - - -
7A THR* 3.8 17.8 - - + +
28A PHE* 5.5 1.8 - - + -
33A PHE* 3.8 42.2 - - + -
78A TRP* 3.9 13.2 - - + +
80A GLY 3.2 11.5 + - - +
81A LEU 3.2 1.0 + - - -
82A ASN* 1.3 77.0 - - - +
84A VAL* 1.3 59.9 + - - +
86A THR* 4.5 0.2 - - - -
87A GLY* 2.7 28.1 + - - +
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Residues in contact with VAL 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A GLU* 3.0 24.3 + - + +
6A ARG 3.4 25.4 - - - +
7A THR* 3.8 13.8 + - - +
83A VAL* 1.3 79.4 - - - +
85A LYS* 1.3 65.2 + - + +
87A GLY* 3.9 0.7 - - - -
88A ARG* 3.2 24.3 + - + +
120A SER 3.7 11.1 - - - +
121A ASP 3.9 4.0 - - - +
122A SER* 3.6 36.6 - - - +
123A VAL* 4.1 9.4 - - + +
126A ALA* 4.1 9.9 - - + -
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Residues in contact with LYS 85 (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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5A GLU* 4.3 0.4 + - - -
82A ASN* 3.5 24.1 + - - +
84A VAL* 1.3 81.4 - - + +
86A THR* 1.3 62.7 + - - +
88A ARG* 3.2 12.2 + - + +
89A VAL* 3.1 34.6 + - + +
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Residues in contact with THR 86 (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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31A LYS* 3.7 32.3 - - - +
33A PHE* 3.8 18.8 - - + -
81A LEU 4.8 1.0 + - - -
82A ASN* 3.0 26.6 + - - +
85A LYS* 1.3 74.3 - - - +
87A GLY* 1.3 67.2 + - - +
89A VAL* 3.1 11.4 + - + +
90A MET* 3.0 26.9 + - + +
97C ALA* 4.9 15.6 + - - +
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Residues in contact with GLY 87 (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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7A THR* 5.4 1.1 - - - -
9A ILE* 5.2 7.6 - - - -
28A PHE* 4.3 21.8 - - - -
33A PHE* 5.0 0.6 - - - -
83A VAL* 2.7 25.4 + - - +
84A VAL 3.9 0.4 - - - -
86A THR* 1.3 72.4 - - - +
88A ARG* 1.3 60.8 + - - +
90A MET* 3.3 5.2 + - - +
91A LEU* 3.1 31.8 + - - +
119A GLY* 6.2 0.7 - - - -
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Residues in contact with ARG 88 (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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84A VAL 3.2 15.2 + - - +
85A LYS* 3.3 16.6 - - + +
86A THR 3.1 0.2 - - - -
87A GLY* 1.3 74.1 - - - +
89A VAL* 1.3 64.9 + - + +
91A LEU* 3.4 13.4 + - - +
92A GLY 3.2 26.3 + - - +
94A THR* 4.8 2.0 + - - -
105A ARG* 5.4 1.3 - - - +
118A HIS* 5.0 1.2 - - - -
119A GLY* 2.7 33.6 + - - +
120A SER 3.5 13.2 + - - +
121A ASP* 3.7 27.7 - - - +
160A GDP 2.6 44.4 + - - -
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Residues in contact with VAL 89 (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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85A LYS* 3.1 31.1 + - + +
86A THR* 3.1 12.7 + - + +
88A ARG* 1.3 75.4 - - + +
90A MET* 1.3 64.0 + - + +
92A GLY* 3.4 10.3 + - - -
103A THR* 3.5 14.0 - - - +
97C ALA 5.8 3.6 - - - +
99C SER 5.0 5.4 - - - +
100C LYS* 4.4 23.3 - - + +
101C PRO* 3.7 24.8 - - + +
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Residues in contact with MET 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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27A ARG* 3.5 39.7 + - + +
28A PHE* 4.0 30.3 - - + -
31A LYS* 4.2 16.4 - - + -
33A PHE* 4.0 23.8 - - - -
86A THR* 3.0 22.9 + - + +
87A GLY* 3.6 8.1 - - - +
88A ARG 3.2 0.2 - - - -
89A VAL* 1.3 79.0 - - + +
91A LEU* 1.3 58.1 + - - +
103A THR* 3.3 6.8 - - - -
104A ILE* 2.9 30.9 + - + +
101C PRO* 4.0 16.6 - - + -
106C GLY 5.3 3.6 - - - +
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Residues in contact with LEU 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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9A ILE* 4.8 4.0 - - + -
28A PHE* 4.3 9.4 - - + -
87A GLY 3.1 26.2 + - - +
88A ARG* 3.6 16.8 - - - +
89A VAL 3.3 0.2 - - - -
90A MET* 1.3 75.7 - - - +
92A GLY* 1.3 59.8 + - - +
103A THR* 3.9 0.7 - - - -
104A ILE* 3.7 13.0 + - + -
105A ARG* 3.0 60.0 + - - +
117A ILE* 3.6 36.1 - - + -
118A HIS 4.0 3.4 - - - -
119A GLY* 3.6 34.8 - - - +
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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