Contacts of the strand formed by residues 18 - 25 (chain X) in PDB entry 3HI6
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 X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8X GLY 3.4 26.7 - - - +
9X GLY* 4.2 0.7 - - - -
10X GLY* 4.0 18.2 - - - +
11X LEU 5.9 0.2 - - - +
12X VAL* 3.7 28.3 - - + -
17X SER* 1.3 78.6 - - - +
19X ARG* 1.3 64.4 + - - +
20X LEU* 4.2 0.9 - - + -
81X LEU 3.5 1.4 - - - +
82X GLN* 3.5 4.5 + - - +
83X MET* 2.8 56.4 + - + +
86X LEU* 4.0 3.8 - - + +
116X VAL* 4.0 15.3 - - + -
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Residues in contact with ARG 19 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8X GLY* 3.7 19.6 - - - +
18X LEU* 1.3 79.0 - - - +
20X LEU* 1.3 69.8 + - - +
21X SER* 4.2 8.3 + - - -
71X SER* 5.3 1.8 + - - -
80X TYR* 3.5 51.0 + - + +
81X LEU 3.4 10.3 - - - +
82X GLN* 3.6 22.1 + - + +
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Residues in contact with LEU 20 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7X SER 3.5 5.8 - - - +
8X GLY 3.8 23.6 - - - +
9X GLY* 3.9 8.1 - - - +
18X LEU* 4.2 1.1 - - + -
19X ARG* 1.3 79.7 - - - +
21X SER* 1.3 62.5 + - - +
36X TRP* 3.6 25.8 - - + -
80X TYR* 3.3 7.8 - - - +
81X LEU* 2.9 35.6 + - + +
83X MET* 3.4 35.2 - - + -
94X TYR* 3.6 38.6 - - + -
114X THR* 4.1 9.0 - - + -
116X VAL* 4.2 2.5 - - + -
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Residues in contact with SER 21 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5X LEU 4.3 0.2 - - - -
6X GLU* 3.2 5.5 - - - +
7X SER* 2.9 46.4 + - - +
19X ARG* 4.2 10.2 + - - -
20X LEU* 1.3 75.0 - - - +
22X CYS* 1.3 61.6 + - - +
23X ALA 4.3 0.9 - - - -
36X TRP* 3.9 2.8 - - - -
78X THR* 4.4 4.5 - - - -
79X LEU 3.4 5.4 - - - -
80X TYR* 3.5 25.7 - - - -
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Residues in contact with CYS 22 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4X LEU* 3.7 25.8 - - - -
5X LEU 3.3 7.0 - - - +
6X GLU* 4.6 0.4 - - + -
21X SER* 1.3 77.2 - - - +
23X ALA* 1.3 60.3 + - - +
24X ALA 3.7 1.2 + - - -
29X PHE* 5.1 0.9 - - - -
34X MET* 4.7 0.7 - - - -
36X TRP* 3.8 9.9 - - + -
77X ASN 4.0 0.2 - - - +
78X THR* 3.4 4.7 - - - +
79X LEU* 2.8 43.7 + - + +
96X CYS* 2.1 52.9 - - + -
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Residues in contact with ALA 23 (chain X).
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 5.0 7.4 - - - +
25H SER* 4.3 20.3 - - - -
26H GLY* 4.5 9.6 - - - +
3X GLN 3.9 0.9 - - - +
4X LEU* 3.4 4.7 - - - -
5X LEU* 3.0 41.3 + - + +
21X SER* 5.4 0.4 - - - -
22X CYS* 1.3 70.3 - - - +
24X ALA* 1.3 59.1 + - - +
25X SER* 5.2 0.5 + - - -
77X ASN 3.9 4.7 - - - -
78X THR* 4.3 11.4 - - + +
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Residues in contact with ALA 24 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24H ALA 4.1 1.4 - - - +
25H SER* 3.8 12.9 - - - -
26H GLY 5.0 0.2 + - - -
77H ASN* 5.8 0.2 + - - -
3X GLN 3.5 5.2 - - - -
4X LEU* 3.5 16.4 - - + -
22X CYS 3.7 1.6 + - - -
23X ALA* 1.3 73.4 - - - +
25X SER* 1.3 64.3 + - - +
27X PHE* 3.6 11.0 - - + +
29X PHE* 3.4 38.8 - - + -
77X ASN* 3.0 26.3 + - + +
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Residues in contact with SER 25 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5H LEU* 6.0 0.3 - - - +
23H ALA* 4.1 15.6 - - - +
24H ALA 3.6 18.2 - - - -
25H SER* 4.0 11.3 + - - -
76H LYS 5.0 1.6 - - - -
77H ASN* 6.1 0.2 - - - -
1X GLU 4.4 1.3 + - - -
2X VAL* 3.4 1.4 - - - -
3X GLN* 2.9 54.0 + - - +
23X ALA 5.2 0.5 + - - -
24X ALA* 1.3 75.8 - - - +
26X GLY* 1.3 63.5 + - - +
27X PHE* 3.3 8.7 + - - +
77X ASN* 5.8 1.6 - - - +
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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