Contacts of the strand formed by residues 39 - 45 (chain H) in PDB entry 5I2D
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 39 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29H ARG* 4.3 17.3 - - - +
31H VAL* 4.2 21.1 - - + -
32H GLU 3.6 21.1 - - - +
33H LEU* 4.2 17.9 - - + +
37H GLY 3.6 2.9 + - - +
38H ARG* 1.3 75.3 - - - +
40H ILE* 1.3 60.2 + - - +
66H GLU* 5.6 5.4 - - - +
143H GLU* 5.4 5.0 + - + +
147H ASP* 2.8 48.0 + - - +
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Residues in contact with ILE 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104G GLU 4.5 0.2 - - - +
105G ALA* 4.4 11.0 - - + -
108G GLN* 3.3 47.6 - - + +
31H VAL* 3.3 7.1 - - - +
32H GLU* 3.1 47.5 + - + +
34H LEU* 4.3 23.8 - - + -
38H ARG* 6.2 0.4 - - + -
39H LEU* 1.3 76.6 - - - +
41H THR* 1.3 72.3 + - - +
42H LEU* 3.4 17.7 + - + -
103H TYR* 5.4 0.4 - - - +
147H ASP* 3.9 7.4 - - - +
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Residues in contact with THR 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29H ARG* 2.8 41.6 + - + +
30H VAL 4.3 1.8 - - - +
31H VAL* 3.7 5.4 - - - -
40H ILE* 1.3 77.8 - - - +
42H LEU* 1.3 60.4 + - - +
43H ARG 4.0 14.8 - - - +
44H HIS* 3.8 31.4 - - + +
103H TYR* 2.7 30.6 + - - +
107H LEU* 5.2 0.2 - - - +
119H TYR* 5.4 0.8 + - - +
144H GLU 4.5 0.3 + - - -
147H ASP* 3.0 22.8 + - - +
148H ALA* 4.0 5.0 - - + +
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Residues in contact with LEU 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G GLN* 3.8 31.0 - - + +
104G GLU* 2.8 40.5 - - + +
105G ALA* 4.4 4.7 - - + +
30H VAL* 2.6 18.0 + - + +
31H VAL* 3.9 6.5 - - - -
32H GLU* 3.6 20.0 - - + +
40H ILE* 3.4 28.9 + - + -
41H THR* 1.3 74.7 - - - +
43H ARG* 1.3 59.5 + - - +
63H TYR* 3.4 47.1 - - + -
100H VAL* 3.8 0.2 - - - +
103H TYR* 3.1 8.2 - - - -
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Residues in contact with ARG 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97G MET* 4.1 19.4 - - - -
101G GLN* 3.1 23.4 + - - +
11H TYR* 5.6 0.6 + - - -
29H ARG* 3.6 3.1 - - - -
30H VAL* 2.9 54.8 + - + +
41H THR* 3.6 4.6 - - - +
42H LEU* 1.3 82.2 - - - +
44H HIS* 1.3 74.2 + - - +
45H VAL* 4.0 4.0 - - - +
50H TYR 3.7 2.0 + - - -
51H PHE* 3.5 21.0 - - - +
53H GLU* 3.0 42.0 + - - -
93H LEU* 5.8 1.0 - - - +
96H GLN* 3.1 33.4 + - - +
100H VAL* 3.8 21.8 - - + -
103H TYR* 4.7 4.3 - - + -
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Residues in contact with HIS 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27H LEU* 4.6 13.5 - - + -
28H VAL 3.8 3.8 - - - +
29H ARG* 5.4 0.4 - - + -
41H THR* 3.8 23.7 - - + +
43H ARG* 1.3 83.3 + - - +
45H VAL* 1.3 58.0 + - - +
46H LEU* 5.1 1.3 - - + -
68H MET* 4.6 18.3 - - - -
96H GLN* 5.0 0.7 - - - +
99H ARG* 2.7 30.8 + - - +
103H TYR* 4.2 22.0 - + - -
119H TYR* 3.0 41.4 + + - -
122H PHE* 3.7 33.6 - + + -
123H LEU* 4.7 4.5 - - + -
148H ALA* 4.3 0.4 - - + -
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Residues in contact with VAL 45 (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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23H LEU* 3.3 14.7 - - + +
27H LEU* 3.3 5.4 - - - +
28H VAL* 2.8 48.2 + - + +
30H VAL* 3.8 28.0 - - + -
43H ARG* 4.0 11.4 - - - +
44H HIS* 1.3 73.4 - - - +
46H LEU* 1.3 65.2 + - - +
49H ASP* 3.7 20.9 - - + -
51H PHE* 3.8 38.1 - - + -
96H GLN* 4.3 1.8 - - - +
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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