Contacts of the strand formed by residues 33 - 39 (chain H) in PDB entry 2JIX
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 TYR 33 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32H TYR* 1.3 81.5 - - - +
34H TRP* 1.3 64.8 + - - +
50H TYR* 3.4 41.7 - + + -
51H ILE 3.6 2.2 - - - -
52H GLY* 3.7 19.1 - - - -
54H GLU* 5.0 7.8 + - - -
56H SER* 5.0 8.4 + - - -
97H ARG* 3.8 0.9 - - - -
98H GLU* 2.8 49.1 + - + +
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Residues in contact with TRP 34 (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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2H VAL* 5.9 3.6 - - + -
4H LEU* 4.0 10.2 - - + +
24H VAL* 4.1 19.4 - - + +
27H ALA* 5.4 3.6 - - + -
28H SER 3.7 6.3 - - - -
29H ILE* 2.6 57.7 - - + -
32H TYR* 3.3 45.5 - + + -
33H TYR* 1.3 73.9 - - - +
35H SER* 1.3 60.4 + - - +
50H TYR* 2.9 6.5 - - - +
51H ILE* 2.7 48.4 + - + +
52H GLY 5.8 0.2 - - - -
53H GLY 5.4 0.4 - - - -
78H PHE* 3.2 44.6 - + + -
96H ALA 3.1 22.9 - - - -
97H ARG* 3.4 26.0 - - + +
98H GLU* 4.2 1.6 - - - -
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Residues in contact with SER 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34H TRP* 1.3 75.7 - - - +
36H TRP* 1.3 68.9 + - - +
37H ILE* 4.1 4.6 - - - +
47H TRP* 3.9 7.6 - - - -
49H GLY 3.1 15.9 - - - -
50H TYR* 4.5 0.2 - - - -
78H PHE* 4.1 2.6 - - - -
95H CYS* 3.4 3.8 - - - -
96H ALA* 2.6 54.5 + - - +
98H GLU* 2.9 38.4 + - - -
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Residues in contact with TRP 36 (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* 3.3 23.6 - - - -
20H LEU* 4.0 15.9 - - + -
21H THR* 3.9 22.9 - - - -
22H CYS* 3.9 0.7 - - + -
35H SER* 1.3 76.8 - - - +
37H ILE* 1.3 59.3 + - - +
47H TRP* 3.9 1.6 - - - -
48H ILE* 2.8 43.1 + - + +
49H GLY 3.3 6.1 + - - +
69H ILE* 3.5 27.4 - - + +
78H PHE* 3.5 33.2 - + - -
79H SER* 3.8 10.0 - - - -
80H LEU* 3.4 53.6 - - + +
93H TYR* 4.8 3.6 - - + -
94H TYR 3.3 20.9 - - - -
95H CYS* 3.5 16.8 - - + -
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Residues in contact with ILE 37 (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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35H SER* 4.1 12.6 - - - +
36H TRP* 1.3 74.6 - - - +
38H ARG* 1.3 61.6 + - - +
45H LEU* 4.1 6.5 - - + -
46H GLU 3.2 19.1 - - - +
47H TRP* 3.5 28.9 - - + -
93H TYR* 3.8 1.6 - - - -
94H TYR* 2.9 33.1 + - + +
96H ALA* 4.2 14.4 - - + -
102H ILE* 4.3 11.2 - - + -
103H GLY 4.9 0.2 - - - +
106H TRP* 3.5 40.2 - - + -
98L PHE* 3.7 29.2 - - + -
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Residues in contact with ARG 38 (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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37H ILE* 1.3 77.2 - - - +
39H GLN* 1.3 64.2 + - - +
40H PRO* 4.1 7.1 - - - +
44H GLY 3.7 0.7 - - - +
45H LEU* 3.6 2.6 - - - -
46H GLU* 2.7 84.1 + - - +
48H ILE* 3.6 20.5 - - + +
63H LEU* 4.0 23.9 - - - +
82H LEU* 4.3 4.2 - - - +
88H ALA 5.4 1.1 - - - -
89H ASP* 3.4 30.7 + - - +
91H ALA* 3.7 13.4 - - + +
92H VAL 3.4 4.5 - - - -
93H TYR* 3.1 42.8 + - + -
94H TYR* 4.8 0.4 - - - -
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Residues in contact with GLN 39 (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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38H ARG* 1.3 76.4 - - - +
40H PRO* 1.4 65.7 - - + +
41H PRO* 3.9 1.4 - - + +
42H GLY* 5.3 6.7 - - - +
43H LYS 5.1 1.3 - - - +
44H GLY* 3.5 22.3 - - - +
45H LEU* 3.8 20.1 - - + +
91H ALA* 3.3 2.9 - - - -
92H VAL* 2.6 45.5 + - + +
94H TYR* 3.3 19.7 + - + -
38L GLN* 3.2 40.8 + - - +
87L TYR* 3.4 16.0 + - - -
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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