Contacts of the strand formed by residues 13 - 18 (chain H) in PDB entry 3IT8
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 13 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55G LEU* 3.7 16.2 - - + -
123G VAL* 4.1 20.4 - - + -
8H PRO* 5.3 1.3 - - + -
11H LYS 3.1 11.0 + - - +
12H PRO* 1.3 74.4 - - - +
14H ALA* 1.3 79.4 + - - +
36H LEU* 4.1 19.5 - - + -
38H ALA* 3.0 39.8 + - + +
39H ASN* 4.4 7.0 - - - +
41H VAL* 3.2 8.4 - - - +
154H ILE* 3.3 13.7 - - - +
155H ILE* 3.5 22.4 - - + -
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Residues in contact with ALA 14 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123G VAL* 5.7 0.2 - - - +
13H VAL* 1.3 84.4 - - - +
15H HIS* 1.3 61.4 + - - +
16H VAL* 4.9 1.1 - - + -
36H LEU* 3.3 15.3 - - - +
37H LEU* 4.0 7.9 - - + -
41H VAL* 3.6 23.3 - - + -
48H LEU* 4.2 13.5 - - + -
59H TYR* 4.2 1.7 + - - -
153H GLY* 2.8 4.8 - - - -
154H ILE* 2.8 42.2 + - + +
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Residues in contact with HIS 15 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93G LEU 4.9 2.0 + - - -
94G LEU* 4.7 0.4 - - - +
122G GLY* 4.3 1.8 - - - -
123G VAL* 3.7 16.9 + - + +
124G PHE* 3.6 26.0 - + - -
14H ALA* 1.3 74.8 - - - +
16H VAL* 1.3 61.2 + - - +
17H VAL* 5.5 4.5 - - + +
34H ASN 3.7 20.0 - - - +
35H ALA* 3.3 11.9 - - + +
36H LEU* 2.8 44.2 + - + +
59H TYR* 2.6 26.8 + + - +
151H TYR* 3.4 47.9 - + + +
152H PHE 3.6 3.1 + - - -
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Residues in contact with VAL 16 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H ALA* 4.9 0.2 - - + -
15H HIS* 1.3 79.2 - - - +
17H VAL* 1.3 62.2 + - - +
28H TRP* 3.6 30.5 - - + -
29H LEU 3.3 14.4 - - - +
30H ASN* 4.1 7.2 - - + -
36H LEU 4.0 11.0 - - - +
37H LEU* 4.8 2.7 - - + -
43H LEU* 4.0 19.1 - - + -
48H LEU* 4.1 19.1 - - + -
151H TYR* 3.3 6.3 - - - +
152H PHE* 2.8 58.9 + - + +
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Residues in contact with VAL 17 (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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15H HIS* 4.2 4.5 + - + +
16H VAL* 1.3 75.0 - - - +
18H ALA* 1.3 67.0 + - + +
28H TRP* 3.5 5.9 - - - -
29H LEU* 2.8 53.6 + - + +
32H ARG* 4.3 24.2 - - + +
35H ALA* 5.0 7.2 - - + -
147H SER 3.6 21.5 - - - +
148H GLY* 5.3 2.0 - - - -
150H VAL* 3.0 22.9 - - + +
151H TYR* 4.7 4.9 - - + -
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Residues in contact with ALA 18 (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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17H VAL* 1.3 87.4 - - + +
19H ASN* 1.3 63.5 + - - +
20H PRO* 3.4 12.5 - - - +
26H LEU* 3.7 13.7 - - + -
27H GLN 3.5 5.6 - - - +
28H TRP* 3.7 4.1 - - + -
29H LEU* 3.3 2.8 - - - +
32H ARG* 5.2 0.3 + - - -
144H PHE* 4.1 20.8 - - + +
150H VAL* 3.2 38.0 + - + +
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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