Contacts of the strand formed by residues 45 - 52 (chain H) in PDB entry 2QQK
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 45 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37H VAL* 3.7 18.8 - - + -
38H ARG 3.5 1.8 - - - -
39H GLN* 4.1 29.6 - - + +
44H GLY* 1.3 72.6 - - - -
46H GLU* 1.3 60.2 + - - +
91H TYR* 4.5 6.3 - - + -
103H TRP* 4.2 13.0 - - + -
36L TYR* 5.4 1.6 - - + -
38L GLN* 4.7 0.9 - - - +
44L PRO* 4.2 22.2 - - + -
87L TYR* 3.7 36.8 - - + -
98L PHE* 3.7 51.1 - - + +
99L GLY 4.8 3.0 + - - +
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Residues in contact with GLU 46 (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 VAL* 3.5 3.1 - - - -
38H ARG* 2.8 76.2 + - + +
44H GLY 4.8 2.2 - - - +
45H LEU* 1.3 75.0 - - - +
47H TRP* 1.3 75.1 + - - +
48H VAL* 3.4 4.0 - - + +
60H ALA* 5.4 2.1 - - + +
62H SER* 3.1 26.4 + - - -
98L PHE 6.1 0.2 - - - +
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Residues in contact with TRP 47 (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 HIS* 3.0 20.4 + - + -
36H TRP 3.9 9.6 - - - -
37H VAL* 4.0 6.3 - - + -
46H GLU* 1.3 81.6 - - - +
48H VAL* 1.3 59.0 + - - +
49H ALA* 3.3 22.6 + - - -
50H TYR* 3.0 33.4 - + - -
58H ASP 3.7 22.9 - - - -
59H TYR 3.7 2.7 - - - -
60H ALA* 3.4 45.9 - - + +
100H MET* 3.5 25.4 - - - -
95L LEU* 4.1 20.0 - - + -
96L PRO* 3.6 38.9 - - + +
97L THR* 5.1 1.1 - - - +
98L PHE* 4.2 15.8 - - + +
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Residues in contact with VAL 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H TRP* 3.0 34.1 + - + +
37H VAL 3.8 0.9 - - - +
38H ARG* 3.6 23.3 - - + +
46H GLU* 3.4 16.8 - - + +
47H TRP* 1.3 75.8 - - - +
49H ALA* 1.3 64.6 + - + +
59H TYR* 3.5 1.2 - - - -
60H ALA* 2.8 32.6 + - - +
63H VAL* 3.5 20.2 - - + +
67H PHE* 3.9 32.1 - - + -
80H LEU* 4.9 1.8 - - + -
90H TYR* 4.7 7.9 - - + -
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Residues in contact with ALA 49 (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 HIS* 3.3 1.6 - - - -
36H TRP* 2.9 24.1 + - + +
47H TRP* 3.3 12.4 + - - -
48H VAL* 1.3 84.0 - - + +
50H TYR* 1.3 64.7 + - - +
58H ASP 3.2 15.9 - - - +
59H TYR* 3.6 22.4 - - + -
69H ILE* 4.3 13.7 - - + -
80H LEU* 4.6 13.2 - - + -
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Residues in contact with TYR 50 (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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73A ASN* 5.1 0.2 + - - -
75A HIS* 5.6 0.4 - + - -
34H ILE 3.2 13.7 - - - +
35H HIS* 3.4 29.6 - + + +
47H TRP* 3.0 22.7 - + - -
49H ALA* 1.3 75.3 - - - +
51H ILE* 1.3 61.4 + - - +
52H TYR* 3.7 25.6 - + + -
56H TYR* 3.9 18.3 + + - -
57H THR* 3.2 26.7 - - - -
58H ASP* 3.1 37.5 + - + +
69H ILE* 3.3 9.3 - - - +
100H TYR* 3.8 22.2 + - - -
94L TYR* 2.5 34.7 + - - +
95L LEU* 4.3 0.2 - - - +
96L PRO* 3.9 2.9 - - + -
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Residues in contact with ILE 51 (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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33H GLY* 3.6 0.9 - - - -
34H ILE* 2.9 45.6 + - + +
50H TYR* 1.3 76.3 - - - +
52H TYR* 1.3 86.7 + - + +
55H GLY* 4.7 7.2 - - - +
56H TYR 3.3 5.6 - - - +
57H THR* 3.5 23.8 - - + -
69H ILE* 3.4 20.2 - - + +
70H SER* 3.6 31.2 - - - +
71H ALA* 3.7 19.1 - - + +
78H ALA* 4.8 2.7 - - + -
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Residues in contact with TYR 52 (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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74A PRO* 3.9 10.5 - - + -
75A HIS* 3.1 25.9 - + - -
32H TYR 3.9 1.1 - - - +
33H GLY* 3.6 20.2 - - - -
35H HIS* 4.2 3.3 + - - -
50H TYR* 3.7 29.1 - + + -
51H ILE* 1.3 75.1 - - - +
52H PRO* 1.3 58.9 + - - +
53H ASP* 3.3 3.1 - - + -
54H SER* 3.1 18.0 + - - +
55H GLY* 2.7 32.4 + - - -
56H TYR* 3.0 28.5 + + - +
95H GLU* 2.6 24.9 + - - -
97H PHE* 3.4 40.2 - + + -
100H TYR* 3.9 6.6 + - - -
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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