Contacts of the strand formed by residues 18 - 25 (chain H) in PDB entry 3INU
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 18 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9H GLY* 4.3 28.7 - - - +
10H GLY 3.9 16.4 - - - +
11H LEU 4.6 3.1 - - - +
12H VAL* 3.5 34.3 - - + -
17H SER* 1.3 77.7 - - - +
19H ARG* 1.3 64.3 + - - +
80H LEU 4.0 0.5 - - - +
81H GLN* 3.8 4.2 + - - +
82H MET* 2.8 53.0 + - + +
109H VAL* 4.0 11.9 - - + -
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Residues in contact with ARG 19 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8H GLY* 4.0 15.2 - - - -
9H GLY 4.5 1.1 + - - -
18H LEU* 1.3 78.0 - - - +
20H LEU* 1.3 72.7 + - - +
21H SER* 4.1 2.3 + - - -
70H SER* 4.9 3.8 + - - -
79H TYR* 3.7 45.0 - - - +
80H LEU 3.4 7.4 - - - +
81H GLN* 3.3 36.9 + - - +
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Residues in contact with LEU 20 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7H SER 3.8 3.8 - - - +
8H GLY* 3.9 1.1 - - - -
9H GLY* 3.4 35.4 - - - +
18H LEU* 5.2 0.4 - - + -
19H ARG* 1.3 78.4 - - - +
21H SER* 1.3 62.6 + - - +
36H TRP* 3.8 24.5 - - + -
79H TYR* 3.4 5.7 - - - +
80H LEU* 2.8 38.8 + - + +
82H MET* 3.5 32.1 - - + -
90H TYR* 3.5 37.7 - - + -
107H THR* 3.9 13.5 - - + -
109H VAL* 4.1 2.0 - - + -
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Residues in contact with SER 21 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H GLU* 3.4 3.6 - - - +
7H SER* 2.8 51.5 + - - +
8H GLY* 5.1 0.2 - - - -
19H ARG* 4.1 3.3 + - - -
20H LEU* 1.3 73.1 - - - +
22H CYS* 1.3 62.3 + - - +
36H TRP* 4.2 4.9 - - - -
78H LEU 3.3 5.2 - - - -
79H TYR* 3.3 34.3 - - - -
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Residues in contact with CYS 22 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H LEU* 3.5 28.5 - - - -
5H LEU 3.4 8.7 - - - -
6H GLU* 4.2 5.2 - - + -
21H SER* 1.3 76.9 - - - +
23H ALA* 1.3 63.0 + - - +
36H TRP* 4.1 4.0 - - + -
76H ASN 4.1 0.2 - - - +
77H SER* 3.2 7.3 - - - -
78H LEU* 2.8 41.0 + - + +
92H CYS* 2.0 48.9 - - + -
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Residues in contact with ALA 23 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H LEU* 3.5 0.9 - - - -
5H LEU* 2.7 52.7 + - + +
22H CYS* 1.3 77.8 - - - +
24H ALA* 1.3 63.8 + - - +
25H SER 3.9 0.7 + - - -
75H GLU 5.5 0.9 - - - +
76H ASN 3.6 5.6 - - - +
77H SER* 4.1 9.4 - - - +
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Residues in contact with ALA 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3H GLN 3.5 5.2 - - - -
4H LEU* 3.6 19.9 - - + +
22H CYS 4.1 0.8 - - - -
23H ALA* 1.3 75.3 - - - +
25H SER* 1.3 60.3 + - - +
27H PHE* 3.6 23.1 - - + -
29H LEU* 4.1 9.0 - - + -
76H ASN* 3.0 42.0 + - - +
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Residues in contact with SER 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1H GLU 3.2 3.5 + - - +
3H GLN* 2.9 62.4 + - - +
5H LEU* 5.0 6.4 - - - +
23H ALA 3.9 1.6 + - - -
24H ALA* 1.3 74.4 - - - +
26H GLY* 1.3 61.4 + - - +
27H PHE* 3.3 8.9 + - - +
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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